Decent theory. I think you're right.Incorrect.
While, it's true that she won't walk in on you if you choose "Maybe, but I want a turn with the mask." (she'll stay to clean up and then wait for you in the cafeteria), if you choose either of the other options, and you let Isabelle convince you to continue, you'll tell her to go get the key, and she will walk in on you at the very end of it. (This is true even before 1.40, tested on 1.39)
The real "problem" is that the new quest says she did walk in on us even if she didn't, and as you said, even if it never happened. I say "problem" in quotation because the reason is that the quest is WIP, and, when it's finished, will probably be either completely different, or not activate at all, if she didn't walk in on us.
... And I say "probably", because in the Flora quest "Squid Game" there's a line of dialogue that refers to something that never happened if you're doing the love route, but that's much less of an oversight than an entire quest revolving around something that never happened.
Just played that part today and that part of plot really got me confused. Hope the devs will fix this plot hole soon.