A ground loop or supply loop can equally induce noise because this encourages the flow of DC current between components in the signal path. The engine noise is always present but normally you do not give it an inroad to audio.
All grounds are common. However, it may be important that the source ground is heavier, shorter and direct to the ground point closest to that of the amplifier(s).
The same thing would apply to the B+ side. This would include both the ign/acc and the memory. Sometimes you have to remove these supplies from the factory harness and go direct to the same point as the amplifier(s) supply.
But the biggest issue is that all audio electronics are wired to the output post of the dual battery switch and do not go battery direct. This totally eliminates any possibility that the amplifier could access one battery and the source unit could access the other battery (which will often have varying voltages). With any voltage differential, current will flow through the path of least resistance, and you do not want that path to be the audio path.