Honestly, I think most orientations and gender disorders are usually pretty genetic and ingrained, but I believe that looks and appearance have a LOT to do with how open and confident one is about it. Generally speaking, the hot boys are the ones who don't get any "flack" at school for coming out as gay or Trans, while the ugly boys are the ones who are always picked on for those very same words - I got picked on so much in high school for being gay at the time - even by other gay boys. There were so many gay boys who, just because they were so much hotter than me, were tremendously popular and very open about their sexualities. Then there were the gay boys who were so extremely ugly that they had like a in-denial sense of confidence and were confident none-the-less. I'm speaking about gays here because Trans people didn't really exist in my school.
Like me, I'm as masculine as can be, I have extremely male features, and male features that even are very ugly compared today's "hot" male (Aston Kutcher, Justin Bieber, Johnny Depp, ect ect). I look more like Jack Black. I'm extremely self-concious about Transitioning and Dating, and people who don't even know I'm Trans call me ugly all the time, even when I dress as a natal male. I have a pretty horrible confidence. I am not transitioning at the moment. I just find it impossible beyond any sort of reason.
However, when it comes to if some boys transition just because they were born looking like a girl, I don't think that's true. If it was true, Justin Bieber (and every one of his genetic clones - there's about 5 in every middle school/high school classroom, his genetic makeup and physical features are extremely common among young boys) would have claimed they were Trans a long time ago. However, these guys indeed end up being the most confident out of Today's male generation (long gone is the sportsy, buff, athletic man - everyone in today's world thinks of that type of man as being a "douchebag".) So wether they're gay, straight, or Trans, the cute, petite, model-esque males in today's world usually are always the most popular, confident, and open about whatever it is they may go through internally.