Having a common version for all the files on the repository can also be an advantage. For instance, on multifile packages, you don't have to worry about incrementing the version number on the main file every time you change any other one.

Maybe. If you only ever have one package in your repository, and you don't mind your version numbers getting incremented by tags and branches.

To me the repository version and the module versions are completely different concepts and keeping them separate is the easiest solution.