People should basically use their common sense here. A man who considers himself female but still has all the physical attributes of a man should use the male bathroom. A woman who considers herself to be male, and has gone through the necessary surgery to be a man should also use the male bathroom. Essentially, people should determine which bathroom they use upon the basis of their present body, not the one they wish they had. Obviously, the birth certificate stipulation here doesn't allow for that, so that should definitely be examined upon practical grounds.
This is shockingly progressive from you, Cassius, but my question is where do you draw the line. Most trans men haven't had the genital surgery; would you make them use the women's restroom.