I use NixOS in a Parallels VM, the system configuration files are in nixos directory.
For dotfile management, I use chezmoi instead of home-manager. I've used home-manager for several months, it causes more trouble than solving problems. Besides as I'm the only user for my nixos, installing software as normal user via home-manager makes no difference for installing globally.
I don't install programming language development tools globally, instead I use Nix Flake for per project development environment setup.