After I run the wizard and complete the steps/test is the fixture de-embedded?
Yes, because the reference standards include the same loss as the DUT traces.
Note: if Autoset timebase is enabled (by default), then the TDT delay through the first DUT is used to set the time/div scale. But if the DUT has high loss and/or poor frequency response, the autoset may have trouble. In that case, recommend measuring the thru cal trace (if available) as the first DUT. If through cal trace not available, recommend setting the timebase manually (on the Wizard, before clicking start). That will help the Wizard get the right timebase setting, and it also provides a "sanity check" because the S21 should be very close to zero.
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