Any derived work of something, like git, which is GPLed, must be GPLed. That means that if you fork, the main branch, the main branch is free to use your extensions. This makes it difficult for replacement to work.
I think that neither the on-disk nor wire protocols of git have special copyright protection. If it so chose, Microsoft could develop a fully closed-source git implementation from scratch that is "fully compatible" with, say, git1.8 but has proprietary Windows extensions.