As her son noted, "Gender is a social construct." Not caring much about it is simply rejecting cultural demands to fit into a binary box with rules that have been devised by other people - in favor of just being yourself. He's still biologically male.

There are literally infinite ways to be "a real man" that each guy can and should define for himself. Chucking patriarchal norms of what being male is supposed to look and feel like is a good thing. Instead of worrying so much about whether or not he's accepted into a binary box, Holden (and millions of other young people) are chucking the box and saying that other people don't get to define them.