Well, my opinion is that the gender I was 'supposed' to be was male.
I simply see no way to argue anything else, if you have a Y chromosome you were 'supposed' to be male. HOWEVER nature messes up what's 'supposed' to happen all the time.
So, to answer your actual question first. If I could change it so my soul (or whatever) ended up with a female body right from the start, yes I would do it unquestionably. I can't speak for anybody else, but this whole thing has made my life utter hell. Would I have been a very different person if I had just been born genetically female, of course, my experiences have made me who I am. However call me selfish, but I just don't think its worth it. And honestly I don't see it changing. I lost my entire adolescence while watching everyone else live theirs because of this. No matter how good my life does or doesn't get in the future, nothing will undo that loss, so I don't think my opinion will change.
However in spite of that, I would NEVER go back and change things to make it so I was gender congruent (happy being male).
I can imagine being born genetically female and still being me, a different me, but still me.
I can't imagine being born a mentally congruent male and that person even remotely resembling me. It feels more like I would be dying.
But yeah, to answer your question very simply, yes I would without hesitation.