That makes sense, but a lot of the same points apply. No one thought J.D. was a girl or told him he was delusional for believing he wasn’t. I do get that it was obviously meant to be demeaning there, but almost certainly not for a “you aren’t who you think you are” way, but rather “girls are silly and you’re silly so you’re a girl” way. Casual misogyny: not really better than casual transphobia, but still a separate thing.
The distress JD feels when belittled thusly isn’t because someone really believes he is wrong and bad for thinking he’s a man, but because Cox doesn’t respect him as a doctor and has the erroneous belief that calling him a woman’s name conveys that somehow.