Having local commits intermingled with an upstream code base can make for really hairy upgrades, but I guess every situation is slightly different.
Well we don't put them in git, we put them in perforce because git keels over if you try and stuff 10GB of binaries into it once every few months.
I think the real question is the other way around though, why _not_ use git for versioning when that's what it's supposed to be for? Why do I have to verison some things with git, and others with npm/go build/pip/vcpkg/cargo/whatever?