I don’t know the answer to many of your questions, hopefully others will chime in, but a couple of points…
Did you remember to mod the txshield for 3.3V operation? We had to do that when we used them on the Nucleo boards and I imagine you’d need to do the same with the Due. There are some pics of the mod in this thread.
I believe the phase calibration compensates for the time difference between consecutive ADC samples. analogRead() on a standard AVR Arduino takes a little over 100 usecs but it’s probably a whole lot faster on the Due, so I wouldn’t expect the absolute number to be directly comparable.