I think you're over-thinking it.
The tone will be a little different, a smaller muffler is usually louder, and just using the outside fittings should be sufficient. You should also be able to find a piece of make-up pipe at an auto parts store and just trim it to fit. I've cobbled pieces in occasionally.
Scientifically, the pipes are a turbulent flow anyway, and the little bit of lip on the pipe isn't going to make an appreciable difference in either direction.