This is probably not what you were looking for in terms of the best setup for loading up a rack but we have a Bajarack long with a mesh floor and the high sides. When the kids were little and we didn't camp on trips they would hang out up there for lunch breaks etc. On our last trip we had combinations of bungee cords, zipties and ratchet straps holding everything down. It aint pretty but it did the job, we were adding stuff along the way so having options helped. Trying to figure out a better system but I like the flexibility of being able to strap down whatever whenever. The black bag held all our camping gear and it stayed dry through a lot of rain. The bag is cheap and easy to store but a pain to pack neatly and then strap down well. It surprises me how much room there is on the rack.
I see someone at the kids school who has the same white truck as me with the long Bajarack but I was just driving up highway 85 for 5 minutes and saw 4 4runners each with a Gobi rack, those racks are common as muck round here.