That honestly sounds like an implementation detail compared to figuring out what version control model even makes sense to begin with
If you want local configs, worst case you can update $HOME inline and make it use different dotfiles. If ssh is a must, sshfs can be a way to achieve that
not being able to set ssh parameters (and key paths, etc) via .ssh/config was a nightmare on git a long time ago. impossible to not leak identities to random servers. impossible to have curated identities for the same remote. imposible to use adhoc jump hosts. etc.
If you want local configs, worst case you can update $HOME inline and make it use different dotfiles. If ssh is a must, sshfs can be a way to achieve that