Can you find a company that makes boxes for commercial uses and sells them in bulk? Maybe there are two shoe-box sizes you could standardize on. In the US, I would google “boxes” and “bulk” Something like this.

You’d want to print out a picture of the shoes inside to tape to the end of the box.

There once was a style of plastic shoebox with “wings” that let you easily slide out the one in the middle. But I’m having trouble finding it again.

There arefoldable plastic shoe boxes