I installed this cover last week and have been trying to t it as water tight as possible. Added weatherstripping in the 1" Gap at tailgate a d that's working pretty good. Latest rain storm I went out and had alot of water dumping out the rails at the back of the truck as my truck was parked in the driveway and sloped to rear. The drains they provide are for the front near the cab. After researching it seems they used to provide these for the rear. I emailed them to see if they still carry the part
I'd be worried about that seam running the length of the bed. Without the rambox there's a rubber that cover that seam and rests on the bed toprail. Mine is covered in storage otherwise I'd post a pic.
I don't have rear rail covers either but the piece of rubber I'm talking about helps that rail from filling with water in the first place.
I've never gotten anywhere near the amount of water you are.
I just looked at your Pic again. Now I get it. Yours does not have the rubber so you can open your Rambox lid.
I would still look into sealing that area. I really believe that is the main problem. Maybe you could stuff some foam backer rod they use when caulking deep cracks in there. Really cheap experiment.