RE: Exhaust
Yes, the OEs spend millions in R&D. One of the goals with a factory exhaust is to minimize interior noise while still allowing enough flow to make power. It's a delicate balancing act. On this car, I would rather have the "right sound" on the outside, even if that means more noise on the inside. There is a good reason I opted for the upgraded stereo system!
As far as the exhaust system is concerned (post cat on a 6-speed R/T), I would be willing to bet that I have not altered the flow numbers by much at all. The OE front mufflers are straight through. The Flowmaster Super 44s I installed have internal baffles to direct flow and change the sound. The OE rear mufflers/resonators are what quiet most of the sound on the R/T. I removed them and replaced with OE size tubing (2-1/2") and used the original tips. This cannot amount to any measurable change in emissions averaged over the entire RPM range. Obviously it sounds different. That was the intended goal from the outset. Performance? I would bet it is no different. If anything, I might expect to sacrifice a smidge of low end power for a tiny gain at higher RPM. Only a before and after on the dyno would say for sure, but I would be willing to be that the difference is nothing in the real world.
As for voiding warranty:
If the service guys at the dealer wanted to be schmucks, they could say anything they wanted. In the end, a call to Chysler Customer Service would set them straight. It shouldn't come to that. Technically speaking, altering the exhaust behind the converters does NOT void the factory warranty. It would be one ugly day in the service department if they ever tried to tell me different.