Personally, I stopped worrying about dotfiles and GNU stow after joining the cult of Nix. While I gave honest attempt to everything else, Nix made it stick. Now I only have one single repo, where In write config for (almost) all of my applications in Nix, deploy them with Nix, rollback with Nix etc. Compared to hodgepodge of INI/YAML/TOML/XML/JSON/WHATHAVEYOU it is nice to to only have single tool to worry about.
I wished Guix had the momentum and size of Nixpkgs. I'd much prefer a Lisp than the language contraption of Nix.