Earlier quoted context omitted.
I use stow. But honestly, I don't think it's better than git.
It's orthogonal, isn't it? You keep your dotfiles in a repo, then have stow "install" the checkout/clone thereof. EDIT: Also on stow - I tried it a couple times and it never seemed flexible enough. Can it handle things like keeping ~/.config/nvim and ~/.vim in the same stow directory? (And for that matter, can it link them together? I like having the same config for vim and neovim)
Then when you run `stow vim` from the parent of the original 'vim' folder it will symlink everything in there to ~.
You can even have more folders that have a '.config/foobar' inside of them, and when you stow those it will all work itself out nicely!
Edit: You can find examples of this in my dotfiles https://github.com/AnthonyWharton/dotfiles/ (I use stow if you didn't guess :P). For example look at the 'i3' folder and the 'polybar' folder, they both add things to '~/.config '