My Dad also ran this kind of setup since before I was born. I've used it as well, many times.
For the shelf that rested on top of the bed rails, Dad would take a full sheet of plywood and cut it to length to fit across the bed (65" or whatever) and then rip it in half lengthwise to end up with 2 pieces at 65"ish x 24". He would leave those pieces stacked on top of each other unless he needed the room that both pieces provided.
Dad also kept a full sheet of plywood covered in lime green shag carpet on the bed floor to keep the noise down and provides some padding for all of the kids riding in the back. We also layed out our sleeping bags on the carpet board when camping.
As an adult, I did the same thing. I took my whole family on a week long camping trip and we all slept in the back of the truck, under the shell. THe 2 older kids (5 and 8) slept sideways up on the shelf, and the youngest slept on a futon mattress with me and the wife. We carried all of our stuff in the bed of that truck for a week. No adventure trailer in tow. This was also a shortbed truck, but I'm kinda short.
The futon mattress was a bit thick for fitting under the shelf once you had people laying on top of it.
We never had a problem with water getting in, other that condensation.
For retaining bins on the shelf, you could use a smaller cargo net. I have 3 of these, and they are much more manageable the the larger ones.
24"x36" PowerTye® Mfg Extra Large Cargo Net featuring 10 Adjustable Hooks & Tight 2x2 Mesh, Black
https://www.amazon.com/dp/B00AECG828/ref=cm_sw_r_taa_Yl01xb091PMV2