-- Last Updated: Sep-24-12 10:11 AM EST --
Apparently the answer is "no", since you are happy with your method.
The first answer posted is one good reason for using special racks. Another is that plastic kayaks easily get dented at the points of contact with the rack (I've been noticing all this summer that nearly all the rec boats I see strapped to cross bars with pool-noodle padding have deep dents in the hull). A lot of people wouldn't like this, even if it were only the top deck with dents. With racks having a lot more surface area, denting will only happen to the boats of those careless folks who cinch things down way too tightly. Many boats can be hard to tie down firmly enough that they don't slip and wander around on the roof rack, especially longer boats or if the spread between bars isn't much (too little spread is a very common situation on today's cars). Form-fitting racks are the easiest way to deal with that problem. Finally, some kayaks are light and somewhat fragile, and tying them tightly enough to keep them in place on such a tiny amount of surface area (you won't find a "flattish" contact point anywhere on most "good" boats) would be inviting damage, which is a bad thing since lightweight boats are not "disposable" like so many plastic ones are.
By the way, pipe insulation doesn't provide any real padding, just scratch prevention and some extra "stickiness". The cross bars I use when carrying more than one boat are made of 2x4s, and lack carpeting at one end to allow placement of clamp-on, home-built mounting brackets for J-hooks. When carrying two canoes, one gunwale of one boat rides on that bare wood, so I place a bit of pipe insulation around the gunwale at each contact point. I don't make the tie-downs all that tight, but even so, when the foam pieces are removed afterward they only have the thickness of heavy paper (thus, used on normal cross bars, the padding does virtually nothing to increase contact area. You wouldn't notice this on insulation permanently attached to the cross bars, but you wouldn't miss it when looking at a removable piece right after use).