The same problem pertains if I walk around in a convincing bear costume.  What is changed is your appearance, not identifiable facts used for identity purposes.  In situations (and let's hope they are few and far between) when there is a need to ensure you are who you say you are, you want those papers to say "biological male" if chromosome pair 23 is XY.  Presentation, and who you feel you are (what is going on inside your head) is valid and important, but not particularly useful for identity purposes.  Again, maybe there is a need for a "gender" field on those papers, but I would want to give that a lot more thought before providing such (What goes on in my head is not the government's business, but maybe this is an exception).