@kaarme i think Amane just views Sakura as a woman, even if Sakura isnt trans Amane probably still sees them as a woman in his mind due to the fact trans people tend to be critical of other peoples gender variance and see people like Sakura as "trans, but they dont know it yet"
i think the reason Amane was still confused romantiacally towords Sakura as a boy, is because Amane still technically considers Sakura a woman even if they look like a boy. hence the confusion
its kinda like if you liked a girl, and you were dating, but they dressed up as a guy and they pass really well... will you just not be attracted entirely? no, more then likely your attraction will waver in confusion but wont really go away since you "know" they are a girl