Something I occasionally try to get across is that the Doctor is genderqueer even by the standards of his own people. The often-reblogged quote from Interference (“You’ve never been a woman, have you?” “I’m not sure I’ve ever even been a man.”)—he’s talking to another Gallifreyan there. He’s not just saying “I may never have been exactly what a human would think of as a man” given the anatomical and cultural differences of their planet, but “I may never have been exactly what you, a fellow Gallifreyan, would think of as a man.” As casual as I.M. Foreman is about her new form, she’s still taken off guard by the extent the Doctor has never really felt secure in his ostensible gender identiy. He’s (I go back and forth on what pronoun to use for the Doctor, which I think is appropriate) an eternal outsider in his culture.