For the loose stuff rattling around, cut strips of dense foam to fit the compartments. The stuff they use for kneeling pads or camping mats works fine. Cut it slightly wider than the gap so it stays put from friction alone, no glue needed. When you want to change the layout you just pull it out and cut a new piece. Offcuts of wood fail becuase they're rigid, so they work loose as the tote flexes and things settle. Foam compresses instead, which is exactly what you want. A cheap utility knife and a straightedge is all it takes to fit it. For pliers and tools sitting in open slots, a strip of foam laid over the top of the row works too, kind of like how machinists store tools in cases.
Another option if you want firmer dividers: friction-fit them. Cut dividers a hair oversized and tap them in with a mallet. They'll stay for years and still come out with a tap from underneath when you change your mind. No glue anywhere.
On leaving it loaded, that weight sitting on the bench isn't the problem. The joints care about the handle lifting and swinging the whole load around, not static weight pressing down through the bottom. Carrying it loaded is what stresses the handle and the bottom joints, and that's unavoidable unless you want an empty tote. If you built the handle well, which it sounds like you did after three tries, you should be fine. What I'd watch instead is moisture. Don't store it somewhere damp with tools in the slots, since trapped steel in wood pockets will rust the pliers over a winter. Mine stays loaded all the time because the whole point is grabbing it and going. Stripping it down between jobs just means you've rebuilt your packing system every time, and you'll stop trusting it. If the joints hold for the first month of real use they'll hold for years.