I checked the schematic here, and USB GND and other GNDs are already connected on the board. So, you don’t need to worry about that.

I checked the schematic here, and USB GND and other GNDs are already connected on the board. So, you don’t have any isolation between grounds. Note that you will only have a "ground loop" if your power supply and USB devices have another common ground (e.g. earth) As long as your "external power source" is isolated (transfo, battery, etc.), there should be no loop.