Your Bolt analogy is a perfect illustration of the situation.
Bolt's starts were weak and relatively slow (yes, because of his height) but he was so much better than anyone else that he still won. Same with Biles. She has trouble controlling her landings but the difficulty is so high that her scores still win.
If there is any controversy over her scores, it'll be because the scoring tables don't adequately reward her for the enormous difficulty she brings. As a one-time hack gymnast at the collegiate level, the stuff she throws down just takes my breath away.