How would it not make sense?
Does it make sense that everytime he changes he looks completely different or has a different accent or different personality?
Changing to a woman makes just as much sense.

Just cause you have seen female timelords, doesnt mean they were female in all their regenerations!

Saunders is a better actress than you give her credit for.
Dont judge her purely on Absolutely Fabulous, as that was a huge pile of cack!