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The TC's have been failing NOT because of software, but from one of many mechanical issues: high torque at low RPM, pump pressure, etc.
How do you know this? Do you have some inside information or access to a software engineer working on the USA Bosh ECM/TCM? Give, man, give... one example of software destroying hardware could be the locking/unlock of the TC, under direction of the TCM.
While we notice the more violent iterations of this, the TC lockup is electronically modulated, according to the FSM. If it's buggy software, excessive slipping can cause extreme heat fatique on the TC clutch, and burn it up to the point where debris begins flowing throughout the tranny, until it clogs the cooler, further destroying other mechanical components. My TC, according to the tech, was blue-black and the tranny pan was full of metal debris. He also stated that the TC had a lot of metal parts rattling around inside when he pulled it off.
BTW, pump pressure on the 545RFE is electronically controlled - there is a pump drive gear, and two other driven pump gears - once pressure is built to sufficient levels, one of the driven pump gears is electronically reduced to keep excessive pump pressure from building. On investigating the Transgo kit, I found that the combination of stronger springs and resistor mod raise the pressure to slightly less than 200 psi, which Transgo recommended as the maximum safe level for the 545RFE. 200 psi was also listed as the max recommended pressure. They recommended not installing the resistor kit for those who were also installing custom TCM software that also raised line pressure or excessive pressure induced problems would occur. The higher pressure, within reason, is supposed to keep more pressure on the clutches, reducing slippage (and with it some of the smooth shift feeling) and prolonging tranny life due to reduced heat buildup.
I'm ready to buy the Transgo and put in on the CRD out of sheer frustration with DC not coming up with a fix for the shuddering on heavy acceleration then cruise. If they can't do it after 18 months, it's not likely they're going to get it done. If they do, the Transgo will be a little extra insurance.
So I believe the tranny problems are a combination of sub-par mechanical components, and bad software exacerbating the cost cutting effect to something DC never intended - that is pre-warranty expiration tranny failures.