Yes, right now Wine implements both using global atoms. Implementing NtUserRegisterWindowMessage is necessary to test it, but we cannot split the user/global atoms namespace yet as it would break many other things.
Atoms are just numbers within 0xc000-0xffff but global vs user atoms have different values for the same numbers. So it's possible that one user atom also exists as a global atom, but with a different string value (or even the same value if really unlucky). The test checks both and status only checks if the number exists (another test checks the atom value).