That overwrites the remote dotfiles. Any workarounds?

I've found lnk [0] to be a nice tool for this. Similar to GNU Stow as another comment mentioned, but plays a bit nicer with git (and, in my opinion, is nicer to use).

Edit: just remembered there was a good comparison of lnk and stow on the HN discussion of lnk from a few months back [1].

[0] https://github.com/yarlson/lnk

[1] https://news.ycombinator.com/item?id=44080514

GNU Stow? https://systemcrafters.net/managing-your-dotfiles/using-gnu-...

Keep the alternate sets in different subdirectories.