I've always carried the kayaks on the hardtop, upside down on foam pads which are actually designed for use with the flat cross bars that come as part of most factory roof racks. I've towed my 17' Alumacraft canoe behind the boat from Owen Sound to Tobermory and back. Amazing what one will do to insure the canine component of the family is able to be ferried to shore through shallow water to answer nature's call. The key was using a bridle fastened to each side of the fore thwarts and experimenting with the length of the tow rope (stretchy polypropylene) to ensure the canoe was in the calm, flat water of the wake. Also some weight in the back of the canoe kept the bow up and tracking was very stable. I was able to tow at 24 mph with no concerns. I think the kayak would be a trickier matter due to the lack of a keel and tie off points for a bridle. If you were satisfied with towing your kayak at a relatively low speed it just might work. Interestingly, the warden and I cut a trip short this morning and headed home a day early due to the weather. We did a quick tour of the Bay Moorings Marina while away and were quite surprised to see the significant percentage of both power and sail boats with kayaks aboard. The variety of tie-down procedures was equally amazing but all seemed to be secure.
I have a pic or two of our system for the kayaks but I just can't get past the album stage of the process you outlined on the Simcoe site. I got a pic (laker) into the album and thought I had copied the recommended URL but the preview failed to show the pic. I know it's me and not the system. I'll see later if I can get it to work here with a pic that shows how the warden has successfully altered the fishing vessel TALISMAN into a bona fide pleasure craft.