The food and hospitality industry faces the same problem as you do: restaurants want to store food in a space-efficient manner, but for decades, a business model in which a mom-and-pop place gets a manufacturer to produce 15 containers of their perfect dimension was not viable. Nowadays mass customization is theoretically possible, but the industry has already solved the problem by a different way: standards.
Specifically, there is the Gastro-norm international standard for food container outer dimensions. (If you read German, click through to the German Wiki article, it is much more detailed). It is similar to the DIN paper sizes standard. Many manufacturers produce containers of these sizes independently of each other. Storage space manufacturers produce racks, cases and display systems designed to perfectly fit a given number of Gastro-norm sized containers. This might be the best solution you are going to find, as it is so widespread that I don't know of anybody trying to use a custom solution.
Note that I have seen these containers mostly used for display purposes in canteens. In this case, they were open stainless steel containers. So I don't know 1) if you can get them in plastic, and 2) if you can get covers for them, especially tight-fitting Tupperware style covers. I don't know if this is a deal breaker for you.
If they don't work, you can probably find a combination of plastic containers and storage cases which are close enough that you are only losing a minimal amount of space when fitting multiple plastic containers into a case, but it will need searching. Still, you're not losing more space than by, say, storing books on a shelf. If you get problems with transportation (containers shift in the box because they're not a tight fit), some reusable package fillers should take care of that.