Here is the funny thing, I ran the MSA X-pipe with the factory mufflers for the better half of four months, I could tell zero difference in tone and volume.
However, since the the MSA X-pipe removes a resonator, this is why I welded in two Vibrant 12" resonators after the X-pipe.
Reactive mufflers (Chambered mufflers) produce a high frequency noise as a byproduct of the sound waves bouncing around those chambers. Some chambered mufflers use fiberglass packing or other forms of absorptive material to reduce this noise (But in most cases it's not enough). Absorptive mufflers do not produce a high frequency noise, and due to their design being a perforated tube and fully packed with absorptive materials, they can remove this high frequency noise, what they fail at, though, is the ability to reduce sound levels, where as reactive mufflers succeed in that category. You could take Flowmaster's most aggressive 3-chamber muffler, then replace it with a Magnaflow of the same case size and the Magnaflow would be noticeably louder by several decibels.
With that being said, if I were to do another exhaust system, I would put a chambered dual-in/dual-out muffler in place of the factory resonator and then at the back, place two small resonators.