How do I configure multiple nixpkgs's instances in flake's

If I have a flake that provides a NixOS config, where I have the following inputs:

    nixpkgs.url = "github:nixos/nixpkgs?ref=nixos-unstable";
    nixpkgs-stable.url = "github:nixos/nixpkgs?ref=nixos-24.11";

and I for example set nixpkgs.config.allowUnfree = true; in my config, and use nixpkgs-stable using this overlay:

nixpkgs.overlays = [(final: prev:
  stable = nixpkgs-stable.legacyPackages.<system>;
)];

will packages from pkgs.stable also allow unfree packages as set in nixpkgs.config.allowUnfree?

No. See step #3 here for your choices, ultimately you have to manually import rather than using legacyPackages:

But generally I wouldn’t recommend mixing stable and unstable.

Thanks, that’s annoying… why would you not recommend mixing them? I only am going to use stable for for example broken packages