Writers use pen names some times, though I don't think that holds true for academic writing.
I have an advanced degree, and made sure all my records were changed before I even started undergraduate. That situation was a little different because I wasn't still wrestling with who I was, and I knew I'd be going for an advanced degree.
If you transition, then at some point you will have to change your records if you want to take your letters (PhD, Masters etc) with you. Its easier to do it before you start, because there are that many less people you have to explain things too, but only if you are sure.
Sam1234