I have cartopped folders for a decade, from Feathercraft and Pakboat. They do fine -- I have found that upright J-racks work best because they transfer the load to the sides rather than putting pressure on the longerons (the front to back long tubes of the frame). Plus the semi-inflated sponsons (the inflatable tubes that give the skin rigidity and add flotation) cushion the skin.
(Never leave a folder in the sun or on a car without releaving some of the inflation in the tubes because the air can heat up and rupture a tube seam. Easy to repair but a pain in the butt.)
Also the way that you run the mounting straps over the loop at the top of the J-racks allows you to strap the boat on without deforming it a lot. But I also hauled my first folder, a Feathercraft Kahuna, for thousands of miles of highway driving on cheap molded foam blocks and it never hurt it. Saddles should be fine -- just don't whale too hard on the tie down straps so that you deform the frame.
Even though folders are much lighter than rigid boats, you still want to be sure to use bow and stern bumper attachment lines. Because the boats are so light they catch wind easily and can shift on the car if not tethered fore and aft.
I've loved my Feathercraft folders but at one third the price the Pakboats are probably the best bang for the buck in any folding kayak. And they are quite a bit easier to set up and really easy to load with gear for overnight trips. You'll love the inflatable seat, too. Nice to have adjustable lumbar and thigh support.
Pull-Up Strap Handle Kit
URCHIN Portable Anchor
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