Well, Nix is independent of Nixpkgs so it would be weird if it used buildEnv from Nixpkgs (though, coincidentally, nix-shell does have dependency on Nixpkg through NIX_PATH, unfortunately).
It looks like this might be Nixʼs implementation: nix/src/libstore/builtins/buildenv.cc at 7829caab49e1541f67e143d190bad7d089e06be0 · NixOS/nix · GitHub
Skimming through the Nixpkgs implementation, I would expect that / would indeed link everything, making the other paths redundant.