I'm not an expert but this is what I understood:
Zplot is able to determine the impedance of the feed cable (if different from pure 50ohm)
It also is able to calculate the frequency dependent loss
This will help you understand what power goes into the cable and what into the antenna.
When you calibrate at the end of the feedline you ignore the cable.
When ignoring the cable (apart from the compensated delay) is ok, calibration at the end of the feedline is ok
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