I don't think you are reading it right. If you look at the diagram in the bottom-right corner of pg. 1, I think that small black dot is the supply line rough-in position. I think they want it 8" to 10" from the centerline of the toilet. The diagram on pg. 3 makes it look like it attaches to the bottom of the tank in the standard way.

I see, yes, too good to be true.

Somebody's gonna come up with such a thing right after I buy a new toilet.

jamies-
You want to have ready access to the water supply valve, and you want to be able to readily see any leaking that might occur at any time at the supply fittings; you wouldn't have that with a concealed supply line. If you had ever installed a toilet -- a rather easy project -- you would also quickly see how concealment would complicate the design of the toilet with regard to how you actually hook up the supply to the toilet when installing it: an external supply hookup is simple, but a concealed hookup could be a challenge in terms of getting it right. Finally, in the specific toilet you are looking at, the "skirt" is the fixed, porcelain base, which is an integral part of the toilet. Concealing the supply would mean uninstalling the toilet when you needed to turnoff the water supply valve. Looking at the link to the guide you provided, it looks like a totally standard installation with the indicated location of the supply stub well to the side.

Step 6 shows a standard setup for water supply line connection. I believe the 'hidden' connection you are seeing is actually the anchor bolt/nut that secures the stool to the floor (one on each side).