It seems pretty simple to me. If you ask me to describe my best friend, I might say he's smart, studied this or that in school, speaks such-and-such languages, likes such-and-such music, and so on. His height and weight would be pretty far down the list of things I find important.

Similarly, we think of our mind as being our "self" in a much more fundamental way than our toes.

If a person is female in their mind but has a male body, it seems very clear that we should consider the former to be their "real" gender. Why should the body matter more or be more fundamental?