For me I got the whole "tomboy" thing going on so I can somewhat relate to you (although I don't wear men's clothing). I wear sweater + worn out jeans + converse + hair in a ponytail (and no makeup whatsoever... heck I don't even know how to wear makeup). I always get "why are you such a boy all the time" and I have also gotten "why don't you get a sex change" as well. I'm fine being a girl but I just like acting like a boy (just cuz). Nobody gets it.
When I was little my parents always bought me boy clothing. My shirts always had cars on them or dinosaurs (I think they were expecting a boy but I turned out to be a girl). I loved bugs and everything about them. I think this may have influenced me to be this way. I still love cars and video games though (and bugs here and there lol). This whole 'girl' thing with the makeup and stuff makes no sense to me. It's like a foreign concept to me.
My self-esteem is really low too. I have a skin disorder which really makes me hate my body. There's nothing I can do about it though... I kinda just have to deal with it.
I also feel just like you. I don't think I deserve anything; not even food. Sometimes I don't eat because I feel like I don't deserve it. I always think everybody is better than me and I'm the lowest of the low.
(^^so basically what all this means is that there are people like you out there. You're not alone

)
But to answer your question:
You need to learn to accept yourself to be accepted by others.
Don't hide yourself. Be true to yourself. If you like dressing up that way so be it. You aren't living to impress people; you're living for yourself!
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"People say nothing is impossible, but I do nothing every day." - Winnie the Pooh