Any paint you use will just scratch/scuff back up. You could go with a truck bed coating spray but again, it will just get scuffed up somewhat...maybe not as much as paint. I'm covering mine with an 'enclosure' for my conversion.
I would paint them and cover it with a plywood box to make a useful shelf. That’s what I did when I outfitted the back of a friends Sprinter. Remind me to paste some pictures of GML Russian engineering at its silliest... admittedly the guy used it as a jungle gym.
You can cover them in helicopter tape if you are attached to the color of the paint. If its just cosmetic for you it's an option to just embrace the patina you get from using the van. I would not add wood. Just limits the space between them if you need to move sheet goods. You could coat them at a bedliner shop like Rhino etc with poly-urea. That's a hard plastic that is sprayed on an cured instantly. You could also have an upholsterer bond heavy vinyl over them. Shame that this can doesn't have molded hdpe or similar caps for the wheel protrusions. Thin ones mated with a bed matt would be useful and clean looking like so many other vans.