I'm not terrifically worried about ground loops as I'm using one of Stu's S/PDIF cards with digital coax running back through the car to my amps. Absolutely nothing I did when I installed the unit into this car would get rid of the terribly loud alternator whine that I had. Nothing. Except's the Eutronix card, that is. I suppose I could still induct noise on the analog AUX signal before going back to digital, but that's not likely to happen. Also, in this board I used a completely isolated i2s DAC chip [PCM5102A] external to the RN52 with it's own highly regulated 3v3 power supply, as I found that the internal audio processing is very poor and highly susceptible to noise, even from UART activity.
I absolutely could make this an internal thing, basically replacing the second hard drive. I suppose that I had never really considered that. The smaller analog/digital Molex connectors at the logic board for the docking connector are still available from Mouser/DigiKey, so I could fairly easily make this a plug and play sort of thing as all of the required connections are in those two harnesses.