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.

Honestly, ensuring very good grounding on any single electronic or electric random piece + their mother in law, is just normal good practice, nothing special about it imo.

If i am not mistaking, currently mb also takes some logic supply from steppers via the connections to the gen3 stepper boards, so mb led still lights up and actually doesnt go off when usb is disconnected and steppers still have power (or maybe it does if its gnd is bad). I guess the status of this issue could be treated differently via firmware, although i think its like that on default variant. Maybe this could be more of an actual issue, but even this doesnt seem to be a problem in practice, at least not as far as i can tell.