`setxkbmap` fails to find layout

As written in Nixos builds a ton of packages instead of fetching them in the cache - #5 by jtojnar, you should not need to replace anything else other than xkeyboardconfig.

You could try checking nix-store --query --tree /run/current-system/sw to see what pulls it in.

That is to be expected as, unlike overlays, system.replaceRuntimeDependencies does not change nixpkgs packages but only replaces them in the final built system path.