The fact that your mom has mocked you about your gender identity first, then again about your taking offense to her first "joke," is what I would call bullying. If she picks on you, and you are hurt by what she says, she has no right to complain when you stand up for yourself—especially when her choice words were "freak boy," which just disgusts me, given that she has told you it wasn't intended as a joke. People aren't allowed to choose how what they say/do is taken or interpreted, which is something my graphic design teacher taught me, too: once you release something into the world, it's no longer yours to interpret for others, and you've lost all rights to demand how someone understands it. I think offensive language is the same way, for the most part.
As for how I'd feel in a similar situation, I'd be pretty sore, just like you. It's hard to say how you're mom's taking all this news, it might be a form of grieving that takes the form of lashing out, but again, it's pretty difficult to tell from where I'm standing, and you'd be the best judge of that. In any case, I'm sorry your mom seems insensitive to your feelings, I know that can be incredibly hard.
