All in One PCB

I would like to understand this better. With the freewheel mod shouldn’t the NC on Cytron be connected to the PWM2 on the main board? And what happens under of that white connector coming to the 3pin HDR? Looking at the codes on boards I assume DIR-DIR, PWM-PWM1, skip NC and then GND-GND? And the white connector doesn’t skip NC hence the different order if using the connector wires? And the order of the pwm2 and gnd soldering holes on AIO B have changed from for example Kaupoi 4.1 Board to accommodate the use of that 3P HDR? Why the recommendation not to use that 3P HDR then?