I’m currently learning home-manager. There are some configuration options that let you define common program configurations in nix (the language). But those options are limited and might even require package installation.
So for complex (or existing) configs withou package management, you can just tell home-manager explicitly to take dot file at path A (in a git repo, for instance) and link it to path B. This will check for overwrites too, so if path B already exists it will yell at you and no write over existing files, so no sweat.
You can also define different profiles per machine, so if you need something different per machine home-manager can let you do that too. And since its nix, you can break out configuration files as you would in any other language to organize you dotfiles however you like.
There might be something clever in home manager for mapping a file path in your dotfiles repo to the same directory relative to your $HOME, but it’s likely you’ll just explicitely write something like xdg.configFile.nvim = { source = ./neovim/init.lua; }, mapping precisely each file in your git repo to the appropriate config location.
Let me know if you have other questions. I’m all aboard on the nixos train so I could be bias.