The 10" rough dimension refers to the distance from the finished wall to the center of the drain flange. The 5½" dimension referred to is the location of the water supply valve measured from the centerline of the flange ( a line perpendicular from the wall, thru the center of the flange.) 5½ works for "most toilets" but models with the skirts, the valve needs to be further off the centerline, in this case I think they suggest 8"
About a year ago, I was visiting my brother in VA. They were in the middle of a big remodel in his house. Naturally I had to "look over" the rough plumbing. It was CPVC, which I do not love, but it was a respectable installation. Then he mentioned that he had speced the Toto's with the skirt. My red light went on. We went to the internet and downloaded the cut sheets, and faxed them over to the plumber. Disaster avoided, because drywall was not in and fix was easy. The surprising thing to me was that the plumbing contractor, who was providing the fixtures, had not bothered to look at the specs before roughing in.
