Alright,
Mark at CLT Duc Tri BMW has told me that they're having a behind the scenes unveiling of the 1098 in Feb. when they receive the first bike. Yellow is in fact the second color of the base model with black being the secondary color on the S version.
I'm second in line on the base model, and instead of waiting around for a yellow model to arrive, I'm gonna go with the red since that is what Ducati is producing first.