> and I also have to manually reconcile options that determinate sets in the nix.conf, by translating them into my nix-darwin config
This is what I used to do to appease the installer before. After some options changed and I was like 'you know what, I'm happy with the ones I set; if I have already built the system before I run the activation script, then it's fine to delete /etc/nix/nix.conf.'.
The Nix-Darwin installer isn't a great option for me anyway because it assumes your darwin-config will live in ~/.nixpkgs/darwin-configuration.nix, but I like to keep it in /etc/nix-darwin/configuration.nix for a more NixOS-like convention.