Sakura tbh is probably transgender too, but is just an egg. (For those not in the know, an egg being someone who hasn't realised or keeps denying that they're trans when they are, in fact, trans). While it's good to respect someone's identity - including eggs who may not be ready to come out yet or ready to accept that they're trans - I feel like this story won't go down a tragic route, I hope. If anything, Amane might just help Sakura realise that they're trans and that it's okay because there's someone there to support them.
Trans women have a far more difficult time finding acceptance from most of society than trans men, so while Amane can feel more okay being out since, for people who don't think of him as a guy he'd just be a "princely/masculine girl", Sakura is in a more difficult situation where they can face humiliation in droves and people will just refuse to accept them outright if they did realise or come out as being trans. Not that trans men don't have hurdles to go over, too, but often the victims of violence and discrimination trend statistically far more on trans women.