Regarding the question you posed in the thread title... I think the reason for that lack of acceptance can matter quite a bit in determining quite a lot of things.
The first line in your post seems to me to be influencing a lot of the way you feel. Self-esteem issues. I get the feeling that it's not so much the fact of being a skinny kid that's bothering you, but more your state of mind that this represents to you. Because of the things you went though. Feelings of vulnerability, humiliation, sadness, helplessness, self-hatred maybe. And I sense that you took all these feelings and internally made them your fault. Told yourself that if you weren't like that then the experiences which happened to you might not have happened, and it would be more likely that they wouldn't happen again. So you did everything you could to get away from that. To be someone else. Someone who could never be harmed in that way again. As you say, "The guy I tried everything to remove from my life."
And to do that you tried to become a different kind of persona. The other extreme, maybe? The opposite to everything which made you feel those feelings and made you hate yourself? But that doesn't feel right, either, I'm guessing. And you're feeling that transitioning will bring you uncomfortably close to that previous emotional state of mind again, the one you thought you'd got rid of.
It's a common thing with self-esteem and bullying. We make it our fault. We tell ourselves that if we didn't give people anything to throw at us then they couldn't throw it. The voice inside turns negative and self critical. Instead of seeing the reality, which is that the responsibility for such actions lies solely with those committing them, and it is not our fault for being a certain way. Be that through looks, actions, mannerisms, preferences, or anything else. But, as is often the case, at that age we aren't emotionally aware enough to see that.
Sweetie, what I think you're fighting is what that skinny kid represents to you. The mental associations you have with that image. The snapshot of your emotional state that you took at that time in your life and attributed to yourself. Blamed yourself for. And honestly... the feelings associated with being bullied are never good ones. It's hardly surprising that you're scared you might experience them again.
I think you're scared of losing your shield and being vulnerable. I'm not entirely sure that your gender is as tied up with this as you think it is. And it's a somewhat different issue which may need some kind of resolution. I feel like maybe your lack of self-esteem may be clouding things more than it should, by attributing an emotional state to a gender, and appearance. And maybe you would have more clarity on how to proceed if you were able to untangle the two.
Sweetie, as Kathy says, this is definitely something to discuss with a therapist. To maybe try and work though. I wish you the best of luck with it. Sincerely. *hugs*