No HQ-WB had the elastic rope. They were all sash cord. The individual elastic loop was what ford used on XD onwards. So they are a Ford thing.
Elastic rope is the way to go for sure. You can pop the rear of the tonneau up without un-doing the rope. The Ford idea were useless. They used to break after about 2 uses.
The tonneau will rub the paint off no matter what you do,but yes the eyelets will do real damage if they have no flap covering them. So if you have a flash paint job/Sandman stickers I would be a bit careful.