It doesn't hide anything related to git. The binary in /usr/bin is there to shat xcode-select works and points to /Application/Xcode.app/Contents/.../bin/git. It's not hidden, it's merely a convenience so that you can actually get git, and stay at least a little up to date. There's nothing hidden about it, and installing new, modifying your path, whatever is done just like you would on any other machine.

The binaries are protected by "rootless mode"/System Integrity Protection, but you can disable this and get full root access to your development machine. Just run "csrutil disable" from recovery mode (It wouldn't really help if you could disable it from a running system).

The only locked down things on OS X are proprietary GUI stuff, such as windowserver or some menubar API's. Regular operation is not locked down.