I'm surprised they did not mention this, though they do not seem all that scientific if you know what I mean. I think they specialize in making things loud and that is about it. When I came back the first time, their recommendation was to put the mufflers in, not an x-pipe or anything else. I now realize they were just throwing parts at it like a bad mechanic.You did not say what you replaced the front muffler with. If you removed it and just replaced it with two pipes, one for each side, then yes, you killed the scavenging effect of the exhaust by going with a true dual set up. This kills the torque produced by the engine and kills the fuel economy as well as makes it very loud.
On the other hand, if you replaced it with an X pipe, not only would you still see the MPG's, you would likely feel the increase in torque from the scavenging effect, and a decrease in sound due to the sound waves bouncing off of each other as the sounds passes through the x. The stock front muffler provides the balance between the right bank and the left bank like an after market h pipe, but does not flow as well as an x pipe.
I just had the resonators on the rear removed and replaced the 4" resonated tips and left the front muffler in place. The sound is minimal on the inside, and noticeably more outside. It sounds great and I still see the same mileage and torque as before.
BTW, I have an 11 Limited 4x2, 5.7 Hemi.
Hate that you spent all that money to find you liked it stock best.
In the end, I am out $350. Cheap price to pay for the lesson learned.