I guess I honestly saw "rewrite" and "regenerate" to be two different things. Like, I imagined "regenerate" to mean that the regenerated cells are genetically identical to the previous ones, while rewritten cells would be different. I was thinking that perhaps the Doctor can survive extremes because he rewrites his cells in tiny ways to adapt to extremes in his environment - so he's not necessarily immune to everything all at once.

Perhaps that's something that happens automatically/involuntarily in response to large threats to his system (extreme cold, great falls), but not lesser ones because it takes up too much physical energy. So he can be burned or knocked out, but still be able to fall a great distance without being killed.

I don't know. I'M TOTALLY MAKING SHIT UP HERE.

Also, I like wihluta's idea about only rewriting cells all at once. That does nicely explain how he can be injured and not heal it himself.