As far as I know, there shouldn't be a difference - you should be able to use both Windows and Linux versions of git without a problem.
The only possible problem I can think of is line endings, and that shouldn't be an issue if you selected the default option when installing Git for Windows ("Checkout as-is, commit Unix-style" line endings).
Personally, I use git for Linux to keep the QMK repo up-to-date and a Windows application to commit my own changes to my layout. Whatever workflow works for you should be just fine.
