This reads similar to some of the issues I talked about
here; how a number of the premises and systems feel clunky in how they're implemented, especially in regards to whether or not it wants to explicitly be a transgender game, where that's unambiguously the major theme and the way you're intended to play it, or a game where that's one possible way to engage with it - and how to give the player room to engage on their own without being drug along a set path
while also dragging them along because it's using the story structure of a forced situation with a particular destination.
As that user pointed out, that major turning point ends up being one where the game is awkwardly and visibly rounding up all the possible ways that you could have been playing it and narrowing things down to a quick and messy 100%/0% situation that relies on a single rogue variable. Not only does it not reflect how a player on an 'odd path' might feel about the situation, it can hit funny for those on one of the major paths as well. That's the game struggling under the way it's structured, both plot-wise and systems-wise.
Since most of these issues stem from how the game is currently trying to bend things like its forced plot structure to work with an emphasis on player control or allowing the variables run wild so that they need to be chased rather than corralling them and having them work together as they should, isolating and solving these disagreements will iron out these tears in the fabric of the story. It would call for rewrites, but I still believe it's more of an issue of structure (meaning it'd be more about presenting what's there in a different way, one that organizes the story in a plot structure that allows it to achieve its aims more efficiently rather than having to throw out a large number of scenes or write a bunch of new variants for them) than content.
