Take a look at many new jon boats. You will find that a lot have similar boxes in the back. The overhead view often looks as if they are the same height as the stern bench, but they don't always. On a G3 1436 I did some work on for a guy last year, the two boxes were a good inch lower than the stern bench.
There for a couple of reasons. First of all, it has some of the strength for the boat. A box like that acts as a gusset both in the transom and floor plane as well as the transom and gunwale plane. Being a formed box, filled with foam, the same rigidity can be achieved with much thinner (read cost effective) material. Furthermore, and the main reason for the boxes today (though possibly not in the era your boat was built), the flotation regulations require, in the case of being swamped, the boat to remain level. Given that the weight of the outboard, fuel tank, and often battery is in the stern, more flotation is needed there, as opposed to spaced out just in the benches.