Ratchet straps are only covering/protecting so much. You just have to break down and get the 'special deal' by getting the topper earlier. There's snow, dirt/dust, theft, etc. to worry about. If you have a dog? Gotta Gotta.
I have the A.R.E. brand and have the swing up windows on the sides. My F-150 has the pop out step so I can access anything on the sides of the box without crawling inside. I also built a handmade shelf about 20" wide that goes across side-to-side and supported from the box bed below. I keep my smaller flat rubbermaid tubs in there with necessity contents (e.g. one has battery cables, tow strap, binoculars, roadway triangles, first aid kit, etc.). I finished the shelf off with some wood quarter-round so everything stays atop the shelf.