I stopped by my favorite garage the other day and got this quick answer.
Take the muffler off and run 2 straight pipes. He claimed it looks great and sounds nice (not too loud).

2006 F150 5.4L 4X4

 

Don't know how it would look but from what I have been hearing straight pipe is going to be very. Did they say they are going to cut the Y pipe and run 2 pipes around the spare out the back? Are they going to put in a H or X pipe? I would look for some sound clip of straight pipe exhaust on a 5.4L before letting them do it. Plenty of cheap good flowing mufflers out there if it is a cash issue. I think depending on where you are the truck might not pass inspection missing the muffler. At least they didn't recommend taking the cats off as well.