I have started to play with colmena just now. One thing that caught my eye is, to be able to override nix.extraOptions one needs to use lib.mkDefault, else both will get written to /etc/nix/nix.conf, e.g:

defaults = { ... }: {
  nix.extraOptions = lib.mkDefault ''
      min-free = ${toString (5 * 1024 * 1024 * 1024)}
  ''