Nix is a purely functional language so, unless you pass pkgs to pwnvim somehow, pwnvim.packages has no way to access the its value, and will still create its own Nixpkgs instance, not sharing the config.
inputs.pwnvim.inputs.nixpkgs.follows = "nixpkgs"; only really ensures that pwnvim flake instantiates Nixpkgs from the same Nixpkgs revision as the top-level flake.
If you want to be able to pass config to pwnvim, the cleanest solution would probably be for pwnvim flake to expose an overlay. Then you will be able to plop it into your pkgs.
Relevant: 1000 instances of nixpkgs problem. There is also Announcing nixpkgs-unfree