@Emiya She's in no significant capacity a man yet. Nobody but herself and Sakura even know of her conflict with her gender identity. It'll take a bit more than that to change her official gender in the eyes of the society. For a person to really be a man, he has to be registered as male in the government database of citizens (or non-citizens in the country, but that's not relevant in this case). Before that, it's up to each individual what to call the transexual, in any particular situation and setting. Amane, however, still acts the role of a girl officially, like at school and even in front of her family, even if in a very tomboyish manner.
And no, I haven't missed the point of this manga. However, the point is different for you and me. I'm not interested in any societal messages it might be carrying. I'm only interested in the pretty funny setting and good character portrayals it has.