That’s certainly a possible danger, I don’t know if it’s a likely one. I’ve previously used flake-compat to make sure that tools and workflows that look for default.nix and shell.nix are still viable in a non-Flake-enabled Nix install.
This is where I’m at too. The required changes lives on a different Git branch because I haven’t finished making nix-darwin or home-manager-on-OSX play nicely yet. I am finding that the Flake pattern is much nicer to work with even as a niv user, so I’m starting to open-source Nix definitions slowly that I would not have considered pre-Flakes.
I’m not on my NixOS host atm but there are some configuration.nix settings about IIRC nix.registry that seem pertinent. It should at least make sure that your system’s nixpkgs input is followed by any other flake you use that does not specify that input precisely, but that does not address overlays, I don’t believe.