From what I understand (which could be wrong, or right based on some things but not others) is that Gallifreyans are agender and just appear as/present as particular genders because reasons. Kinda like Transformers.
Would the Doctor count as "transgender" once #13 debuts? Cause the Doctor has literally gone from man to woman. But on the other hand, I haven't heard of real life trans people flipping back and forth. Or for that matter, regenerating like a Gallifreyan.