I doubt that Dean is intending to say that the R1200S will definitly beat a 999, but that the bike is being billed as a 999 beater. A lofty goal to be sure. However, let's compare 999 specs to potential specs of the new BMW.
The standard 999 is claimed by Ducati to have 140bhp and 80lb/ft of torque.
The R-ST engine is claimed to be 110bhp and 85lb/ft. If a nicely tuned R-S actually put out 120bhp and 85 or 90lb/ft, the engine performance could certainly make for a good competition.
The 999 is listed at 410lbs. If the R-S came in around that number and the wheel base was less than 56 inches, the handling could be on par.
On the track, it would take a hell of a bike to be a 999 beater. On the backroads of the US, I think the torque and user friendly BMW power delivery could make a very fast bike capable of beating a 999.
Would I like for BMW to design and manufacture a full-on crotch rocket? Not really, because in order to do that they have to make the bike like the rest of the other companies: conventional fork setup, conventional engine setup, etc.
That's what they told Ducati in the late eighties. Look what they've done with a non-standard engine configuration and a steel tubed frame. (You're probably be right about the forks though.)

Get your facts first, and then you can distort them as much as you please.
Mark Twain