I think the clunk, I'd call it more like a clack bordering on a clank, is the self energizing slipper clutch switching from engine driving to wheels driving (coasting in gear). I found if your easy on the throttle it's not apparent.
Don't think it has anything to do with the slipper clutch. The S1000RR has a slipper clutch (and a chain drive) and exhibits none of this behavior. Of course I could be full of crap.
If you do a quick Google search on "driveline lash", you'll see about 100,000 results, representing just about every make and model of autos and motorcycles. Chevies in particular were prone to driveline lash. Gear design and longevity is a black art to me (try designing gears for a CH-47 Chinook wich can lift 50,0000 pounds).
Clunking or clanking doesn't necessarily mean anything is wrong or that the drivetrain will exhibit less than optimal wear. I plan on bringing it to the dealer's attention, so I have a documented correspondence trail.
On the way to the dealership to pick up the bike, I purposefully exercised the throttle on the R1200GSA. Sure enough, there was some drivetrain lash. The GTL seems to have more, but that may only seem to be the case because the bike is so **** smooth in every other respect. There are almost no other vibrations or noises, so any form of clunk (or clank) stands out.