Ah, I see what you are asking about.
`NIX_CONF_DIR` [is an `envVar`](https://github.com/kirelagin/nixpkgs/blob/94ccee2937f16e3994d33297079561557e952117/nixos/modules/services/misc/nix-daemon.nix#L297), and all the `envVar`s are `systemVariable`s [now](https://github.com/kirelagin/nixpkgs/commit/94ccee2937f16e3994d33297079561557e952117#diff-fa3c1b3dd281ef722c173d8c5d801d7fR321).