Git repository unique id

The SHA1 key is about identifying the content (of a blob, or of a tree), not about a repository.
If the content differ from repo to repo, then its history has no common ancestor, so I don't think a change-set-based solution will work.

Maybe (not tested) you could add some marker (without having to change all the SHA1) through git notes.
See for instance GitHub deploy-notes which uses this mechanism to track deployments.