The glass thickness setting should not matter, but it most definitely does for the XY Calibration. At 4.7mm, the hex on the V6 nozzle is slightly above the bed during calibration. At 5.5mm, the nozzle drops lower and the hex on the V6 nozzle is the point of contact with the calibration square.
During the testing, I noticed that a new firmware 2.5.10 was available. I did the update, repeated the testing, and the results were identical.
