Turns out these boxes are perfect! Yes, it’s a pain to not have separation between the rows, but you can actually fit a 104-piece key set in a single box. This photo shows a complete set of Big Bone MDA profile keycaps with a layer of thin foam at the bottom to help keep them from flipping around when turned upside down. The lower the profile of the keycaps, the thicker foam you would want to add (even bubble wrap would work for like DSAs). The foam is optional, and not necessary if you won’t be transporting the case.
I also tested row 1 SA keycaps and they fit perfectly with no added foam—the lid just touches the tallest point when closed without adding pressure.
As you can see, even when I hold it vertically the keys stay in place. At $10.65 for a 2 pack, I think this is a very good and super economical way to store keycaps. Now, what to do with all these cardboard boxes and flimsy plastic holders?