Maybe etckeeper fits your use case? It's specifically built for managing /etc files with version control systems. I can't say much about it since I've never used it, though.

I personally symlink/hardlink to my dotfiles repo. You can see an example of it here.

There should be no dotfiles outside of home directories so I assume you mean a config file. In those cases, git and symlinks are a great option. Make a config directory in your home dir and organize it however you want. Include config files for the tools you’re interested in, commit them to git for backups and then symlink/hardlink the file to the expected path for the application.

NixOS does that well. I never quite managed to figure out a solution to this on other distros (which is actually what led me into making the jump in the end).

@gkpy I assume by "dotfiles" you simply mean "config files" as there should be nothing in your /etc/portage directory that's hidden. For all configs I want to backup, I just keep a copy of them elsewhere. As for portage stuff, I just copy my make.conf, and everything in each repos.conf and package.* directories.

If you want to simplify a complex solution to an already simple thing, take a look at bare git worktrees.

NixOS

From lack of a better solution, I would symlink the folder or use stow --target /etc flag if you use stow for managing dotfiles.

but maybe somebody knows a clever way to handle this?

backups

Seems like an odd software choice to create actual dotfiles under /etc. Often files there have much the same name as a user's dotfiles but without the dot. Thinking of things like /etc/profile vs ~/.profile and so on.

Without knowing precisely why those decisions were taken (good reason? ignorance? insanity?) it's not clear what steps to take.

Vaguely leaning towards symlinking or hardlinking but precisely what to do and which way around is still unclear.

Do those dotfiles have your user permissions or are they owned by a system account like root?

Are you talking about the .keep files?

Not a great solution, but my custom set of functions that synchronize the (dot)files just copy them over into a directory preserving their paths within it e.g. cp /etc/hosts ~/.sysbackups/$(hostname)/etc/hosts