None of this makes sence. Basically you had a bad ECM that they are trying to take the blame off Toyota and put it on your so they don’t have to warrenty it.
All ECMs have voltage protection/regulation built into them; bottom line. Even if your voltage drops to 10V on the car, it will still run… barely, but it will run. If you over-voltage it somehow, which also doesn’t seem probable in any way it would pop the voltage protection in the ECM, in a sence “frying” it, even though only 3 or 4 components went bad.
As long as your HU is wired into the factory stereo wiring through the stock HU fuse; that can not be it. If your amp is pulling directly off the battery and fused properly then you are fine (seeing u have a small system and nothing huge). The battery is isoltating and providing a buffer of sorts to the cars main electrical system.
Bottom line: They are blowing smoke up your ass so they can blame u instead of fessing up that there is another issue.