The subject of the 'gender transformation' is a tricky one ...
The thing is, it's not explained who the player character actually is, yet. The game also stops mentioning it by around about Route A11. I believe it comes up briefly with the futa TF, but the intention is to resolve that plot point later.
I've sometimes considered making it a choice with diverging dialogue, but it adds in more work, more translation, and people don't mention it often enough for me to consider writing it out. But, I'm planning to resolve a lot of the unexplained aspects of the game with an area in the desert, maybe it won't be a problem then. Or maybe it'll just be even more confusing ...