Based on what I’ve found when having the chance of asking strong players and a few actual pros about their rules opinions, and what I have read online from rules experts, I agree with your main point that the 1989 Japanese rules were written not as “to have a well-written clear-cut ruleset by which to rule any position, following the specified procedure to the letter”, but more like to give some “general guiding principles explaining all the previous special rulings, so that the principles can serve if new strange positions appear, to create new precedents that are nevertheless coherent with the general principles found to hold in all particular precedents”. This was mainly because of many requests (both from inside Japan and outside Japan) to clarify the rules themselves, as previous written Japanese rules were basically just a long list of precedents by example, without any kind of “general rule” or “logic” explicitly within the rules.
That is, if a new rule dispute occurs, and the precise way to interpret the current written rules is ambiguous or ends up behaving in a “pathological” way, pros actually believe that the referees and rule-makers would have to set a new precedent, and would have the final decision. As far as I know, new “rule beasts” from 1989 are all theoretically constructed: no actual dispute which does not have a clear precedent established in the 1989 rules (like, say, a pseudoseki dispute could be) has occurred in Japanese Professional play, to the best of my knowledge.
There is a very peculiar case in the “Torazu Sanmoku” and similar positions, where in fact the new “general principles” and rationale of 1989 could not explain the historical Shuwa ruling of “3 points” for that position (that ruling follows logically from many other territory rulesets which solve disputes in a similar way to stone counting / area scoring, but not directly from a “purely Japanese territory ruleset”). Since they found that particular example to be the only one of the historical precedents which did not fit with the new general principles, they changed the precedent for that one in 1989.
But going back to your argument, even within the internal logic of the new “guiding principles” specified in the rules, I think that string by string determination is important. Basically the text of all the examples does this (sometimes it omits mentioning some string of stones, like in the example 6, but typically focusing on each string by itself, even when there are single-stone strings). This is crucially important in fact for example 25 (double ko seki) as I said: realistically, we know that “double ko seki behaves as seki and does not affect life and death outside of itself”, that is the Japanese precedent basically. Now, the REASON why that is so, according to the 1989 rules general principles, is that when considering the single-stone-strings (the ko stones) they are DEAD, because they are captured and recaptured infinitely, no permanent stone is established. While the large string of stones in each group is alive as it is uncapturable. This difference is crucial because it is what makes the double ko end up as SEKI, and not just normal life (that difference can change the result of a game, as there is no territory in seki). And I would argue that considering “in example 6, once you show that the 4 stones are alive then it doesn’t matter if the single white stone is dead, we can consider all alive” (if for example the eternal life cycle were the only viable sequence), then that would not be too different from saying “in example 25, once we know that the large groups are alive that is enough, we can count everything as alive including those single stones”, which would be wrong (because then by the seki-definition, it would imply that it is not a seki, as there is no dame between the group of live stones).