I missed the part about the width of your rail in my earlier reply. That is your single biggest issue.
I agree with the idea of laying something up there so they can be flat side by side or against a stacker. After that, bow lines (one for each boat) and double straps.
People have mentioned cockpit covers. I am not seeing a way to secure such that would reliably survive a 600 mile trip on the highway in these boats. At the least, clip the loop to the forward bungie so when if does pull off you donβt lose it.
Unloading those boats is not a big deal. Even with the Hullivator on one side, I still periodically load a 50 pound 16.5 ft sea kayak onto my roof using rollers in season.