I was wrong about a few things. At least in my case, the ECM was NOT touched by the GM dealer. So the BB tune in the ECM is still there (AFM off, rear O2's, etc.). The trans tune is gone, of course (torque management is back). I spoke to a couple of local tuners, all of whom recommended to not mess with the TCM for at least the break-in period. All said it would void the transmission warranty (36mo/100kmi). For those suggesting moving the old TCM to the new trans, this would also void the warranty. I even tried to get them to put a drain plug in the transmission pan. Nope. When we pull the pan post break-in to change the fluid, I'll probably swap on a pan with a drain plug anyway, and keep the original should I have a warranty claim.
Based on the codes I scanned, I think something in the transmission control system, possibly the TCM itself, caused the failure. It was fine up until 3 days prior to failure, when a noise started that I mistook for a bad serpentine belt idler bearing. I had checked the trans fluid monthly, and saw no issues. So I didn't suspect the transmission. Then it started shifting erratically, and flaring, then wouldn't pull, all within a few minutes on the same drive. Postmortem, I scanned multiple codes for "pressure control solenoid" stuck off, which might have been TCM related, or might not have. But whatever happened, it cooked the transmission. I elected to replace the whole thing with a GM upgraded reman. The original made it 141k. This one will hopefully last at least that long.