I have an old 5x10 motorcycle trailer with 14" rail sides. Too short to throw anything larger underneath. I have 3 redwood 2x10s mounted in the common perpendicular fashion on top of the rails.
I have been doing it this way since I've owned this boat. (2002 Willie 1.5). I've gone 300+ miles to Corn Creek with my boat on my trailer, loaded with tables, bags, pads and most any kind of gear, minus the big coolers and dry boxes as well as another boat on top with more "soft" gear.
I've had ZERO issues between my raft and trailer and I'm not gentle with either of them.