Flake-Parts Overlays Not Working

You need to consume the pkgs defined by perSystem using withSystem, something like:

nixosConfigurations.home-pc = withSystem "x86_64-linux" ({pkgs, system}:
  nixpkgs.lib.nixosSystem {
    inherit system;
    modules = [
      ./hosts/home-pc/configuration.nix
      diskoConfigurations.home-pc
    ] ++ shared;
    specialArgs = {
      inherit inputs pkgs;
    };
  };
)
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