Since nixpkgs.flake.setNixPath is enabled by default on any flake-based system, that would clobber NIX_PATH environment variable for everyone using flakes (until the Nix bug is fixed).
Though maybe we could have it set nix.settings.nix-path when nix.channel.enable = false and nix.nixPath otherwise. That would make the clobbering opt-in just like it is now.