It is worth noting that the addition of passing stones in AGA rules makes it so that you can count Territory Scoring and get the exact result of Area scoring, the difference, as I stated above, usually only counting for 1 point difference.
Now, this does not make the rules the same, particularly surrounding superko.
I am aware that both forms of scoring are mathematically identical. In this way they are completely equal. But there is a human factor to territory versus area scoring. Authors write of it, ruleset creators write about it, rule set nerds discuss is all over the internet. Human perception is a big part of Go and of rulesets. The perception of certain situations leads to certain behaviors and interpretations.
As someone who teaches newcomers to Go (locally and a handful on OGS), I see this on a regular basis. I also hear similar questions on a regular basis. I’ve also spent the better half of a year researching rulesets and asking questions in various Go venues all over the internet. It needs to be clear that my reasoning includes “human perception” as a valid point when discussing how Area and Territory are not equal. Area is simply easier to understand. Territory takes longer to wrap our head around.
That is my primary point about how they are not equal. Obviously Japanese, as a territory ruleset, has a lot of unique issues related to the ruleset that makes it unique, and does not necessarily represent Territory Scoring as a whole.
Hence my use of the word illusion.
Getting better at go means understanding the illusion and not be influenced by it. Since being influenced by illusionary advantages makes you a worse player.
AGA rules have their own kinks. Like Japanese, I learned of this on Sensei and began researching it further. There is a reason my guide does not include AGA in it, as it has some grey areas, just like Japanese. Unfortunately, Robert Jasiek did not do a thorough evaluation of the AGA rules 
Indeed. Unfortunately, Go appears particularly difficult for people to wrap their heads around initially, myself very much included. Which is why a teacher introducing Go to someone greatly helps retention of new players in the Go community.
I agree with this point:
However, I do not support the argument made here:
I think there is value to teaching beginners about both area and territory scoring, and how they essentially give strategically equivalent objectives, for the sake of dispelling these illusions and misconceptions. Area scoring and territory scoring are really just two ways of looking at nearly the same thing, so maybe giving both perspectives would help a beginner better understand the objective of the game.
Understanding that these two systems give nearly equivalent results might help beginners with better understanding the strategy of the game. I could also argue that focusing on only the territory scoring perspective might create the detrimental misconception that capturing is a bonus to be prioritized (over the efficient control of territory).
Also, when teaching that unnecessary plays inside one’s own territory is bad, I think too much emphasis is placed on the loss of a single point. Except at the end of game, the loss from essentially passing (by wasting a move) is much larger than one point.
Further, I think a difficulty in teaching Japanese rules to beginners is that one is forced to simplify away much of the complexities in determining life and death (necessary under Japanese rules), which may lead to an incomplete understanding that causes further confusion later when dealing with more complex situations. Resolving a life and death dispute under Japanese rules is quite complicated (to do properly), while under area scoring rulesets, disputes are straightforward to settle by playing on.