I can’t believe it took me this long to find this set of three organizer trays that stack neatly inside a common .50 caliber ammo can (available at any military surplus store, or here on Amazon).
The three sturdy trays contain a total of 22 compartments of varying sizes and can be stacked in any order. The largest compartment runs the length of one of the trays and is large enough to hold a couple of screwdrivers. The organizer is made in the U.S.A. from chemical-resistant polypropylene.
Combined with the toughness of a .50 cal. ammo can, it should be a waterproof and practically indestructible small parts storage solution.