I was under the impression that at least the CRT part was fine to modify. At least, Firefox used to ship a custom version with jemalloc, I think (with the necessary patches checked in as ed scripts so that they could avoid having the original source in the repository).
That may be true. I would have to go back and re-read the licence. In practice I do not think they minded too much so long as you were not claiming it as your own and were just changing it for your program only and not overwriting the ones in the system32 dir.
