The thing is, they don't. Because no one ever put Elliot in the position of literally being told by everyone around her that she was a man, no one ever told her she was delusional and should find a counsellor to investigate whatever trauma might have caused her to have these incorrect beliefs about herself that let her think she's a woman when she's clearly not.
The people complaining don't understand because they think it's at worst as bad as JD saying Elliot has an Adam's apple, and they don't or won't confront the fact that that'snot what they're doing to trans people. And yeah, those jokes were stupid and transphobic and unnecessary, but even then the whole joke is that it's funny she gets upset about it because no one could ever seriously confuse her gender. People can always tell. Right?
They don't understand, and they refuse to consider ideas that would let them, and that's pretty fucking shitty. But honestly? If I could just chalk it up to malice, life would be a lot easier.