I though that this topic may help the designers to get more feedback from their work. I can start this thread with one of my own experience:
I am using Gen 3 electronics,
I experienced a problem with the stepper motor, which was stepping randomly when it was powered.
It turned out that this behaviour was due to noise between the ground of the motherboard and the ground of the extruder board.
It was solved by joining the grounds together.
Therefore, my recommendation would be to use only one power supply for both boards and avoid using the USB supply at all.