Reporting back after a dealer visit. I decided this time to leave the controller and batteries intact (removed compressor and throttle position lever/voltmeter) and leave tucked/zip tied cables just out of curiosity for what the dealer would say. If they asked, I would be forthcoming and tell them about the ESC -- not trying to hide anything here.
Surprisingly, they didn't ask a single question. Part of the maintenance was a battery test, and they didn't even make a note about a wacky battery setup.
Of course, your mileage may vary, as usual. But I thought that was interesting...
Next time maybe I'll leave the compressor in the passenger seat, just for fun