So I went back to the dealership on Friday to meet with the Field Service Technician who came down from Denver. We sat down with the service manager, and started discussing the problem. Naturally the service manager kept referring to how "the BCM is fried" and "the heated seats caused it", and I kept reminding them that we didn't know if either of those things were true yet. They also tried to shift the blame to the auto-sound place, again without knowing for a fact what the problem is.
After about 15 minutes of doing my best to be respectful but firm in my point of view, I provided them a copy of BlackWorksInc's post, along with the wiring diagram. I did not include his username or the forum name, but I did point out that he was an ACE Certified Master Auto Technician for Toyota. They both read it over, stumbled for a minute trying to explain it away, and then decided they should get on the computer and print out the diagrams themselves, which they had clearly not looked at up to this point! The printed out the same one I gave them, along with a "power source" diagram, and a "ground" diagram. The service manager was sure he had found the culprit when he looked at the ground diagram, because "the heated seats and the BCM share a common ground"...
We wrapped up the discussion in the office with my displeasure in the fact that Toyota doesn't allow customers to customize their vehicles before purchase, and they certainly don't allow it after purchase either. The FST said he would do some more research to make sure that putting the BCM from a Limited into my Trail would work, but they both made sure to point out that they couldn't cover it if it stops working in a few months because it's not "stock".
Finally I took the FST out to the vehicle to show him the problem first hand. While we were out there I explained to him that ever since I told the dealership I had installed aftermarket parts, their attitude was one of "blame the customer." I asked him if it was Toyota policy to always blame the customer? I also asked him what the dealership would have done if I hadn't been so honest and said "nope, it's all stock"? Would they have continued to diagnose and find the real problem? Would they have found the same problem, or a different one? Lastly I pointed out that I know how warrantees work, and until the dealership can prove conclusively that the BCM is bad, and that the heated seats caused it, I am still covered.
I'm not sure if any forward progress was made, but at least we didn't go backwards either. Waiting for a call back from the FST via the dealership sometime next week.