While the new frame, swingarm, and engine mounting system has greatly reduced the "flexible flyer" feeling on the new style baggers, there is still some capability to generate a little rear steer. That will always be the case until they eliminate the rubber mounted swingarm pivot (otherwise known as rear motor mounts, trans mount, etc.). Without riding several bikes back to back, it might be rather difficult to determine if that hinge under the seat feeling is normal, or there really is something not quite right on that particular bike. So my first suggestion is to get a ride on a couple similar model demonstrators from your dealer. If your bike seems to be hinged in the middle and the demonstrators do not under the same riding conditions, it's time for the dealer to start doing some real diagnostics.
BTW, make absolutely certain you are running the correct tire pressures. Even a few psi too low can allow the tire to squirm excessively. I believe the late models call for 40 psi cold in the rear, not 36-40 like the earlier bikes. Also, as the rear tire wears and develops a flatter profile, getting up on the edge can also result in some squirrelly feelings. How's the tread wear on your bike, and did you notice the same handling issue when the tires were new?
Jerry