Look at a local arts store or Amazon or such for bead storage. They are dealing with this issue all the time! Maybe there are better ones than what you have been using?
e.g.
https://www.containerstore.com/s?q=beads
I have made small strips of foam if a compartment box doesn't seal each compartment off. Place on lid to create seals when closed.
For an active job, I often use small plastic containers, maybe 3x4 inches with a lid that separates. A box for each subassembly. Most parts simply drop into the bin. Some get put in small bags and put in the bin. And some parts get taped to the inside of the top so I don't lose them. Very helpful, taping parts down. With a clear top to the bin it's easy to see what is under the tape. Use console tape (artist tape).
This is my standard sub-assembly box-
https://www.michaels.com/product/gr...imply-tidy-10584306?michaelsStore=1555&inv=20
I also use plastic bags for some sub-assemblies. Side panels, for example- panel and screws.
If you are talking about storage in the process of a camera, not stock storage, pay attention to screw sizes, gears, etc. in disassembly and photograph everything from five angles. You might find that parts are much more distinct than you realize at first glance. Rollei, for example, used a variety of sizes AND threading so that most screws really only fit in one or two types of places. So jumbling them together isn't as horrific as you might think.