Jamie - The benefit of moving the muffler one way or another is pure speculation on my part but I do believe placement can make a very noticeable difference in resonance. No way for me to guess whether a yet-to-be-installed baffled muffler would sound better in one spot vs another on your boat, and there may not be a lot of choice due to space and access considerations.
I will mention when I upgraded my engines to MPI's from carbed, the higher HP and WOT RPMs required an increase in exhaust size from 3 1/2" to 4" so along with all the other parts I needed appropriately sized new mufflers too. The yard installed a standard Centek Vernatone Round and Y-pipe for each engine which commonly works well but the resonance distortion was unbelievably intolerable in this installation. I brought the boat back to the installation yard and, after talking to Centek, had them swap out for the Vernatone MKII 2-stage Round, which resulted in about a 80-90% improvement over the regular Vernatone and made the boat usable once again . I never experimented with adjusting distances since access is difficult, but always suspected I could further minimize resonance and exhaust vibration. Perhaps the right person at Centek or other muffler mfgr may have some advice to offer about distances and wavelength-resonance for single or twin engine installations?
One other quick point. If you don't yet have external exhaust flappers, as a good start just adding those ( Sierra # 18-4458 for 5-6" ?) can make an appreciable difference in exhaust noise heard by others over always-open outlets. As a side benefit they could help protect against water reversion due to following wake if for some unlikely reason engines cut out at cruise.
