Since the project does not install anything to sysconfdir, you do not even need to patch the source:
--- a/pkgs/development/libraries/libwacom/default.nix
+++ b/pkgs/development/libraries/libwacom/default.nix
@@ -51,6 +51,7 @@ stdenv.mkDerivation rec {
mesonFlags = [
"-Dtests=${if doCheck then "enabled" else "disabled"}"
+ "--sysconfdir=/etc"
];
checkInputs = [