I read through this exchange with some interest, but I decided against checking details and trying it out live (without Git plugin as I don’t see value in using it), because – at least starting out – my number one reason for using git was for syncing. Since iOS doesn’t allow git and Working Copy and A-Shells apps both use libgit2, accumulation of .git per se makes it impossible to indefinitely use git version control on iOS with large vaults and many changes.
So what I do is always create a new repo with my latest vault every few months to keep syncing to mobile without issues.