Because

...Most men are stronger than most women. Obviously not every man is stronger than every woman, but it's a pronounced trend. I'm all for gender equality but let's not ignore scientific facts just to feel better. The other points you brought up:...well, that's up to story themes and such. Magic and super science are common so sudden acquisition of strong secondary sexual characteristics isn't that unusual; even though obviously changing a man's karyotype from XY to XX wouldn't actually accomplish much in real life. So I don't really see the point of the criticism unless it's just that you want to a see a very "realistic" (as far as that's possible) TG story.