Caps in my opinion are a PITA -- tough to crawl around in, make the generally GOOD visibility of a pick-up BAD. With pull-out organizers they can be OK (still hard to see around). Plus anything but the metal ones with shankless padlocks are a break-in magnet.
I have an ARE fiberglass tilting locking bed cover (ya, had I KNOWN there was an app, woulda got the Roll N Lock so I access everything equally well from the top). Most of my tools are in home-made canvas roll-up pouches strapped to my tailgate. With my pouch setup and and two shoulder-slung toolbags, I can move and carry the tools wherever I need to, on foot, which was important to me. (2) 2x4's divide up the rest of the bed to keep gear somewhat organized and not slide around. Currently it's not loaded to the gills but there is definitely space left for an air tank and a couple big "tupperware" containers for more race/towing/travel gear... and I already have a buttload of tools, supplies, 2.5T jack, 20' jumpers, 5G gas can, and other stuff in there. Later when I get to my home computer I can post pics of everything if interested. F150 supercrew (with the "extra short bed").
On the flip side, American Van sells a number of trick (and EXPENSIVE) flat floor-mount toolboxes with long slide-out drawers. A fellow s. FL racer had one of those in his short-bed Chevy with a cap, and it worked pretty well for him. It's just a $$$ box with limited space inside the drawers, e.g., an impact wrench probably won't fit. There are also some law enforcement and hunting supplier that sell $$$ pull-out organizers for the back of trucks, you could look there if you still want a cap. The law enforcement ones are typically lockable and very robust.
Edit: However, if you add up the cost of a "secure" cap, truck, special cabinets/boxes... maybe you just want to consider a van already outfitted with shelves. A Sprinter allows everyone but Lebron to stand up inside, and a DRW/Blue Tec can pull ~ 5,000. Not cheap though.