Most likely this is the case, but it is untested. SD-WACCM runs on 88 vertical levels to match the meteorological fields that nudge it. Free-running WACCM6 runs on 70 vertical levels. It was not tuned for 88 levels, so it is not advisable to run a free-running simulation on 88 vertical levels. There are many compsets available for WACCM6 without SD nudging.