Part of the command instrument rating test includes demonstrated competency at flying an NDB approach. Flying it in LNAV is not proof that the candidate is competent at that task. For the same reason an autoland is not proof that the candidate can manually land an aeroplane. The autopilot does a sterling job of most LNAV features but the skills test is not of the autopilot but of the person. Therefore the candidate is required to prove he can hand fly using normal tracking skills on an NDB and not the artificial "crutch" of LNAV.