Update: I took the rear door (hatch) apart and confirmed it has the orange box ECU unit and all the wires in the assembly look in great condition. The body shop manager did indeed scrap the old door. However, he says they always pull and replace the electronics and wiring of the original units unless they are too damaged during the incident. The new door from LKQ Parts was a '00 SR5 model he thinks, but is checking. So all the wire harnesses and plugs matched. The wire harness of replacement door at hinge area was cut coming from LKQ, so that sort of confirmed he indeed swapped the wiring. All the wiring including the hinge area was in great condition with black tape mostly intact everywhere. Attached is a photo of the ECU unit and P/N checks out for '01 compatibility.
So the question is, like someone asked here, is this unit also the remote receiver for door lock/unlock? Also note, I confirm all functions of door lock/unlock, window up/down with dash switch, window up/down with key, wiper, operate as they should. Just not any remote function. I tried to reprogram myself via youtube instruction, and I hired a keyless remote tech to also try to reprogram. there was never any beep or flash to indicate anything was communicating during the reprogramming. Also, I have the "beeper" in the front passenger fender by the hinge. What's next?
And apparently I need to figure out how to add a photo here