Yes. It comes from the same voice that tells you you aren't good enough, not pretty enough, not ... fill in the blanks enough. I guess the same goes for questioning yourself. However, if this voice gets too loud I would suggest therapy to figure out why it happens. Everyone second guesses, I guess.

there is probably some biological/evolutional benefit for that nasty voice in our heads. But what if that voice would not be there? it is good to have a inner critic, just as having an inner best friend. Both weigh in on your final decision, which is usually the best decision.
When I was 1 year on hormones , one day I realized that: I know I am a woman, because I know what I am not. A Man. It was the breakthrough I sought. Then I asked myself again on the 2 year mark: Okay, some doubts. But would I want to live like a man again, and put on male clothes? Hell no! Since then all doubts vanished.