I don't see a use case where one want to edit a file without having his work being tracked by git, can someone shed a light to me on this?

I understand that to modify a single configuration point (a path, whatever) a configure option is the right way and is not versioned by git, but Modules/Setup is a file, not a flag.

But, I assumed the whole time Modules/Setup modifications are not trivial, but the result of some work worth versioning, unlike a single configure option, am I wrong?