My guess would be the way the "input" and "output" stock pipes are arranged. Without being able to crawl under my truck right now, I'm thinking the suggestion of an "offset in" and "offset out" would be so the muffler can fit right in without modification of your stock pipes, or to allow the muffler to fit without hitting against the frame or other periphery.

A swag guess at this point as I cannot get to my truck at the moment to verify this answer.