Here's my setup for a single sea kayak. I put some formed foam on the adjustable crossbars and since only the bow is touching the front of the rack, there's a 3 mil rubber pad cemented onto the contact point to prevent rubbing off the powder coat.
IMHO, I never had any love for the factory rack. There's simply not enough real estate by comparison to other options. Sure, there's a drop-in model from Baja but that shrinks the basket area even more. That being said, I'm sure you could still tie a hammock to it without issue.