We'll be towing ours behind the motorhome, so we can't really do a trailer. And we'll have the bikes on the hitch, so roof mount is kind of our only option.I've got four yaks, 14' - 17', to transport. An old utility trailer with an extended tongue makes moving boats so much easier that lifting them up on the roof.
You're right, it does seem a little dicey to have them sitting up like that on the J-hooks. I'm starting to think I'm better off strapping directly to the rails like your second pic. Still gotta find the right rack though. My husband is adamantly against rail-mounts, and the available options are $$$Yakima bars. J cradle works but I feel like laying them flat puts less stress on the fiberglass drip rails.