Automatic transmissions tend to keep the RPM's low for better fuel consumption. Most non-resonated aftermarket exhausts drone at a low RPM. With a manual transmission, you can control where you want to shift so you can stay out of the low RPM's if the drone bothers you.What difference does the transmission make for the exaust?
I bet his shop did not realize where the cats are.There are a few with custom exhaust S5Trace but nothing more than cat-back systems. Make sure your shop is aware that it's a matter of an engine drop to get the cats out and I dread to think how difficult it is to get to the headers, it's an extremley tight fit!