Unfortunately timeout griefers would simply move to doing so before passing, as the OP observed.
While appearance is in the eye of the beholder, this doesn’t mean we can’t avoid creating an appearance in the eye of the relevant beholders by avoiding behaviours that contribute to that.
Which is what I advised.
I watch a lot of games in the course of moderating. Case #2 is extremely common. I can’t remember any instance in which it was reported (in contrast to obviously abusive cases, i.e. #3, which does get reported).
The trouble with applying this online is (1) nobody ever asks to resume when it is case #2, and (2) nobody observes the right to play first if that involves making two consecutive non-pass moves on the board. The system doesn’t even easily accommodate it. If it were the requesting player’s turn, he would have to pass, and then if the opponent passed, we would be back at square one.
The Japanese rule is really to accommodate case #1, not case #2 and #3. Do we ever see this occur among pros? Of course not, because pros know how to count. Do we ever see it with amateurs playing IRL? I haven’t, because everyone, pros and amateurs, quickly begin to move the stones around to score the board after two passes (or 3 with AGA rules). Everyone IRL understands that a pass means there are no more useful moves. In that sense, case #2 is inherently abusive unless the player is a beginner, who can’t count and doesn’t really know whether there are any useful moves left.
First time I ever read that this “exception” exists …
Right- no invasive move into territory at end of game and almost every player at my rank is going to have to change.
Almost every player at your rank is able to tell the difference between a move that is likely to be effective and one that is simply timewasting.
If you can’t tell the difference, then your suggested approach does sound safest for you.
Technically, under Japanese rules, it is incorrect to resume play in order to resolve life-and-death disputes (part of case 1).
I believe the official Japanese rules do allow a player to resume a game if they found that they missed something (case 2), but only with the cost of giving their opponent initiative. Of course, I doubt you will ever see professionals or even strong amateurs doing this, but it is part of the rules.
Resolving a life-and-death dispute requires analysis of hypothetical play under a different set of ko rules (essentially the ability to make ko threats is nullified, and instead a player must pass and declare for a specific ko in order to retake that ko). Further, after using such hypothetical play to determine which stones are dead/alive, the board is returned to the original end game state for counting, but just with the status of the group(s) in question appropriately settled. This is such that any additional hypothetical plays do not alter the score (i.e., from playing inside one’s own territory to complete captures).
Players should not be resuming the game for life/death disputes (part of case 1) when using Japanese rules, since it could result in:
Of course, resuming play to resolve life/death is quite common among amateurs, since:
Hence, if anything, players using the official Japanese rules should only resume for case 2 (as well as finishing incomplete territories, which is something that was previously mentioned as part of case 1).
I agree that the system does not appear to facilitate proper resumptions under the Japanese rules, since the opponent should be given the first move upon restarting. Perhaps, that is an argument for updating the system?
I disagree with elements of your interpretation, as the rules are far from unambiguous. Robert Jasiek’s commentary (http://home.snafu.de/jasiek/j2003com.html#Japanese1989Rules) called Article 9.2 “ambiguous purpose of confirmation phase” and “ambiguous determination of ‘end of the game.’” He also called the resumption rule “superfluous.”
In the commentary that follows the rules in the link you cited, a diagram of the game stages contradicts your interpretation, I believe. Under “Game Stops” (i.e., after two consecutive passes), players “confirm” the territory and life and death. Per 9.2 they can then resume play, which logically would relate to a dispute about territory (unfinished boundaries) or L&D. Notably, the text headed “Examples of Confirmation of Life and Death,” which follows the commentary on your link, says at the beginning, "The results in the following examples would be reached through confirmation of life and death if the game stopped in the position shown in the diagram. They do not prevent these positions from being resolved through actual play before the end of the game. This is reiterated in several examples. This occurs in the resumption before the “end of the game,” which follows the resumption of play and should not be confused with the Game Stops phase. Then during the “End of Game” stage, the players “remove dead stones,” “fill in territory,” and “count.” In practice IRL, these two stages occur simultaneously, which I suspect is why Jasiek called the earlier stage superfluous.
I believe this additional material supports my view previously expressed. Most importantly, it definitively shows that resumption is not predicated on counting; it can occur only before stone removal and counting. OGS (and I suppose other servers—I don’t know) does not have a “Game Stops” or “confirmation” phase. It goes straight to stone removal and counting, which constitute scoring. As such it is illegal to allow people to resume play on OGS for the purpose of case #2 under Japanese rules.
The official Japanese rules are the 1989 edition, with an English translation available here: Article 1. The game of go.
What you linked to is the commentary for the so-called “2003 Japanese Rules”, which are not officially sanctioned by the Japanese go association, but rather is the sole invention of Robert Jasiek and represents his opinions and views of how the Japanese rules should be redefined in a very technical manner.
I trust that you understand this, but I just wanted to make it clear for anyone else reading along and clicking on these links, since the “2003 rules” are presented with an air of formality that might confuse some people.
The players have the option of resolving these positions through actual play, however, that might not be the strategically optimal way of handling every kind of position. A trivial case would be if player A disputed that their obviously dead stones were alive, then resuming play for player B to resolve the dispute by playing more stones to capture those dead stones would erroneously reduce player B’s score. Instead player B should demonstrate that the stones are dead without resuming play and needlessly filling in their own territory to capture dead stones.
A more interesting case can arise when there is both a bent-four-in-the-corner and an unremovable ko threat. I talk about how this is handled under Japanese rules in this thread: Life and Death under Chinese Rules (see the end of the first post and post 9). In this case, if there were a dispute at the end of the game, resuming play would be the wrong thing to do, since all that black (for the diagrams shown in that thread) could do is start an unwinnable ko fight. However, the proper way to handle this situation is for black to appeal to the special ko rules during the confirmation stage, which allows him to call white’s position in the top-left dead, while also not disturbing the seki in the bottom-right. This is vital for obtaining the best status and score.
This statement seems a bit unclear to me, but I just want to reiterate that the confirmation of living/dead stones depends on the consideration of ideal, hypothetical play with special ko rules, and is not the same as resuming alternating play with the normal ko rules. Hence, confirmation happens in a “stopped game” state. While the players have the option to resume play (per clause 9.3), that might not be the strategically best thing to do. Again, resolving life/death disputes should not require resuming the game (as done on OGS), since the wrong type of ko rules are applied.
It is difficult to speculate exactly why since he does not appear to fully elaborate on that point on that page. However, we should keep in mind that that is just the personal opinion of one person within the context of arguing for abandoning the official Japanese rules text in favor of his own reinterpretation. Note that he also calls clause 13.1 (both players losing) superfluous, but I think the official commentary provides a reasonable explanation for why that rule exists.
I think determining which stones to remove (i.e., the logical confirmation of which stones are alive or dead) is essential before the mechanical act of removing dead stones and counting. I think maybe the OGS system might not do the best to clarify the distinction, but I would interpret 9.2 as saying that the game only actually ends fully after the players have agreed on stone status and gone through the mechanics of removal and counting. Other commentary attached to the rules text supports that view (see for example the discussion about clause 13.1, where it implies that “agreeing to end the game” is a phase separate from making two passes to stop the game.).
It seems that your declaration of illegality hinges on what I believe is an erroneous assumption that two passes equals end of game, rather than just a stoppage, or that the OGS system necessarily forces this false equivalence. Thus, perhaps your view is letting (the possible limitations of) the OGS system dictate the rules rather than the other way around, which would seem more appropriate.
Since the OGS implementation is not definitive, I wonder if we could ask “what is the spirit of the rules?”
In the case of Japanese rules, the “spirit” is “these rules are supposed to capture what Japanese professionals agree to do”.
Jasiek’s interpretation captures what actually happens (as I understand it): the game is over after two passes (the game enters the hypothetical stage at this point).
The 1989 rules capture what actually happens woefully in a wide range of scenarios, including this one.
So if we want to achieve what ostensibly the Japanese rules set out to achieve: play in the way that Japanese pros do - then we need to ask ourselves “what do they do?”.
My understanding is that they do not play on for improved position after passing, though my experience is extremely limited, so concrete facts would help 
There are two separate points that I am trying to make.
The first point is that properly resolving life and death under Japanese rules is not done by resuming play (with normal ko rules). If a life and death dispute is resolved by resuming the game and playing on, it can lead to an incorrect and hence unfair result. Note: I think it is possible for a player to request a game resumption to resolve a life/death situation, however, they are not compelled to do so (since it might not be in their best interest) and may instead argue for life/death within the stopped game/confirmation phase with the special ko rules applied.
For my second point, which I have not said quite so directly, I think it is difficult to clearly distinguish between a player resuming a game “to clarify life & death or incomplete territories” vs “to seek opportunities to do better spotted during counting”. A player could be doing the latter, while claiming to just be resolving a life and death dispute or clarifying incomplete territories. Further, what is playing on to resolve “incomplete territories” if not “seeking opportunities to do better”? I think it would be very difficult to fairly enforce a distinction across all cases. The current status of OGS is that the resume game button exists for Japanese rules games. Disallowing it to be used under some circumstances might be a bit confusing.
Both @Eugene and @Conrad_Melville seem to be suggesting that the Jasiek 2003 rules should be the authoritative reference for the Japanese rules. Will or should that really be the policy going forward?
Jasiek’s 2003 rules completely ban game resumptions, which I don’t think has been supported by anyone in this thread. Those rules simply state that the game is over as soon as two passes are played, and the only thing left to do is hypothetical analysis to determine life/death and score counting. This hypothetical analysis does not allow incomplete territories (e.g., from gaps in borders) to be fixed, and leaves amateur players in a very tough situation to analyze if they have left a complicated life/death situation on the board. Further, the strict application of these rules require all dame to be filled before passing, since otherwise living adjacent groups would be ruled as in seki and not contribute any territory.
I think strict application of Jasiek’s 2003 rules would be even much more beginner unfriendly than the informal application of the “spirit” of the Japanese rules that we have right now. Further, it would require the resume game button to be removed altogether for Japanese rules games, since there would be no permissible use of that button. If players make the mistake of passing too early, they would simply have to deal with the consequences.
Why in the world are you bringing up Jasiek’s 2003 rules? I never mentioned that, and it has no bearing on this discussion. I quoted some comments that he made pertaining to the 1989 rules. These happen to be on the same page as his promotion of his 2003 rules, but the comments pertain specifically to the 1989 rules. My purpose in quoting him was to show that I am not alone in thinking the 1989 rules are ambiguous. Nothing more. Any other inference is a mistake, or worse.
Further comments may follow, as I do not have time now.
I’m sorry, I don’t mean to misconstrue your intentions if that’s not what you meant.
I discussed them further because you first brought them up by linking to the commentary, and I was under the impression (based on the citation and further remarks) that you were supportive of his interpretation of resumptions being “superfluous”.
To be clear, I would be against adopting the Jasiek 2003 rules as the standard to judging Japanese rules games on this site, since I think they are overly rigid with the procedural aspects (e.g., banning resumptions of any kind, unfilled dame creates sekis, etc.).
While we’re clarifying I too did not mean to suggest adopting Jasiek
Rather, I observed that in respect of game resumption, I was not aware of Japanese Pros doing that to gain advantage, and that is consistent with Jasiek formally disallowing it.
My argument is that our (OGS) interpretation of the rules might be best served by making sure it aligns with the spirit of the rules. Further, the spirit of the rules is “Play like Japanese Pros”. Which leads us to " if they don’t resume for advantage, neither should we".
I think “Play like Japanese Pros” is quite ambiguous and could lead to more debatable issues. I don’t know of a situation where Japanese pros have ever resumed a game after passing, so that would naturally guide us to removing the “resume game” button altogether from OGS, which I do not think has been the expressed preference of anyone in this thread. Also, as far as I’m aware, Japanese pros always fill in all the dame before passing to begin scoring, but a common preference among amateurs is to leave dame unfilled, as a matter of convenience.
Perhaps a better “spirit” to guide meta-adjudication of the rules would be simply “play with respect and practice etiquette”. I think that resuming a game after two passes should be discouraged on the grounds of bad etiquette, but I find it difficult to formally justify that with the written Japanese rules, or clearly draw the line between some of the situations that may fall under cases 1 or 2. Further, I think that being more flexible about when games can be resumed is friendlier to beginners who might be confused by some aspects of the rules.
That’s actually the statement of how we got here isn’t it! 
Generally, this (whole paragraph!) is how the moderators treat these sorts of situations.
It tends to only come to threads like this when someone questions the judgement in a particular case, and someone pulls out the rule book to see what the moderators “should have” done.
Which isn’t wrong or a bad thing in itself - I already learned in this thread (or was reminded) of a lot about what the rules actually say, and learned the opinions of a number of well-respected community members, which is valuable input into tough calls.
Eugene can you DM me?