I think it's a great idea. Anyone cut one open to see the internal arrangement? It would be relatively easy to add a straight through perforated tube with a layer of steel wool and high temp fiberglass.
I would just get the Cherrybomb 'Turbo Thrush' (car) muffler, with the offset inlet/outlet. It looks almost identical to the stock muffler and does almost exactly what you're talking about. You could prob. sell your stock one to pay for it and save a lot of hacking and cursing, lol.
This is the only pic of the Cherrybomb turbo thrush I have, but I'm sure if you do a forum search you'll find more.
But you're pretty much going back to the carbon footprint of a car when you mess with the cat in the stock muffler.
I am no mechanic, but bear with me. I am definitely not going to cut open the stock exhaust like Ninja650rDude, but thanks for doing it, that information was very helpful indeed. What about replacing the headers to say, Arrow or Leo Vince, and then putting the stock exhaust back on; would this improve its performance?