IIRC the 03's are the only ones with a PCM. Pretty sure the 04's have the PCM functions integrated to the ECU.
Theoretically, neither would be a problem as the needed computer would not only have to control the trans but supply readings to the ECU\PCM in the range it expects, even it did nothing with the outputs. A constant CEL from readings being off with the potential for limp mode in the engine is not acceptable. Big part of the issues of retro-fitting is how to seamlessly handle the existing inputs and outputs.
The problem is not the 727/47RE/48RE transmission, the problem is a high TQ medium duty engine mated to a light duty trans that was not designed for the power inputs. It was a compromise to get a functional vehicle at an aceeptable cost.