I do not believe a being could tell if it has a male or female wired brain without relying on some fictitious tropes (or call it stereotypes) about manliness or femininity. This is a constructivistic/social phenomenon.

Well there's two questions. One is whether it's possible for "inner" sex and "outer" sex to be in conflict. There's no reason to think this is impossible.

The other is whether a person suffering from this could tell something was wrong. They couldn't diagnose the problem in detail, but shouldn't they be able to tell, at some level, that something isn't right? Denying the latter just sounds like gaslighting to me.