So, word is she initially was a tranny and internally there was a massive fight over it because they felt it would alienate players, so they ended up taking out any confirmation she was a tranny and left it ambiguous by having an extremely masculine and manly "woman." Also, funny enough, the last part of the game they start to kind of make her seem a little more girly, where it's like the bulk development really tried to emphasize she was a tranny, after mass exodus of Naughty Dog employees over the last couple of years, it seems like they tapered off a bit by the end of the game.