I don't really understand how it works.
Are the git objects encrypted before being pushed? In that case how are they handled by the server? Does it accept them even though they make no sense? What Github is going to show?
The Git repo itself is completely normal in every other respect, so if you push to Github, everyone can still see the entire repo.
This is a good design as it lets people move repos easily and avoid too much lock-in, but it may (will...) come back to bite people soon, who push things to Github thinking they were "encrypted by Keybase", which is not what's going on.