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It's probably personal preference for the most part.
One of my trucks has a muffler, the other doesn't. I do not like the sound without a muffler while my wife doesn't mind either way....so pick what you like.
As far as performance. The truck with the muffler is quicker and stronger. The non-muffler truck is quick to respond off the line but doesn't build boost very fast. The truck with a muffler has more lag but boost hits hard and keeps on pulling. According to AE, the truck with a muffler is .3 seconds quicker from 0-60 mph.
I have not checked either truck for boost leaks yet so that could change everything if one truck leaks boost while the other doesn't...
Don't forget local/state laws. Here in Texas, a buddy of mine tried to get his straight-piped truck through the annual state inspection process...and they spotted it. No inspection sticker for him!