[special-K]

All I can offer is I'm sure all Magnaflow systems are made the same and they have obviously been fitting a lot of trucks. I'd venture to say possibly more than half were likely lowered as much or more as yours. I know shops will use the universal "it's because of that mod you did" card for a cop-out. My eyes are on that shop,too. All brake tabs are in the same place. Are both pipes running parallel with center of truck? Is it possible the passenger side is misaligned further forward causing it to come to the wrong place further back? If I was a shop I'd want to do my own exhaust and not be stuck with someone else' work. That might be coming into play. You don't need a muffler shop to install a pre-fab system. I'd expect a muffler shop to be biased and opinionated about the best exhaust system,how things should be done,etc. than a general repair shop.
I don't know why you can't run pipes straight back along side of the fuel cell under the frame rails or a bit wider. Not that you wanted that and you should have what you wanted...and paid for.