Here is a custom 2002 S3 that looks a lot like an 05 with a single muffler.
I've thought of an under-engine design too, but I'm pretty sure there's not really enough room. The link you sent was for a V-twin, obviously. Let's not go near the whole "just copying Buell" argument by trying under engine silencers.
However, I have had the tail section all apart and I think it is possible to have an undertail silencer, if you can find some place to put the tail/brake light. It would have to be removed.
Another possibility would be two silencers on one side like Ducati.
Just some thoughts.
