Philly, I don't think the restrictions in a muffler (baffles, perforations, etc.) will do anything to aid inertial scavenging. Inertial scavenging is pretty much controlled by the cross section of the header pipe.
The resonant wave can be used to help hold the fresh charge in the cylinder, but IMO, that resonant wave can only be harnessed with an open exhaust system where there is an abrupt change at the end of the pipe (i.e. drag pipe).
If you run a muffler, you want something that changes the cross section of the system or forces the hot gas to turn. That change in cross section, or the abrupt turn, will break up the resonant wave and prevent reversion (drag pipe sag).
This is a good video that discusses drag pipe sag.
https://www.youtube.com/watch?v=KjKUKhHQLHgThat David Vizard system that Fast650 referred to is a pretty cool system. He installs a big empty cannister at the end of the header. As I recall, the cannister must be at least eight times the volume of a single cylinder. The cannister simulates the abrupt change in pressure associated with the end of a drag pipe and also provides a nice big container for the hot gas to accumulate and then bleed off through the muffler. It keeps back pressure to an absolute minimum. It would be pretty hard to make something like that for a motorcycle, but it is a way cool idea. I believe that I might be able to make one from a 4" automotive resonator, or possibly a much longer 3" resonator. Always something to do, something new to try.