There is a specific and detailed guide to setup the speakers properly. They need a hollow surrounding in a special size and that space needs to be completely closed off.
So that space is being used for the hollow surrounding? Could you make a diagram like you did with the nub showing what area under the case the speakers actually take up?
It's standard speaker design. You find out where your speaker's frequency range drops off and tune the case to that frequency. With a high-fi speaker it's usually tuned to the bottom end to extend the bass a bit, but with portable speakers it may be tuned anywhere if there's a specific missing frequency in the speaker's footprint. Theoretically there's also reflections to worry about, as out-of-phase reflections can knock out certain frequencies, and doubled up relfections will boost that frequency, which is why most speakers are filled with foam to soak up direct reflections, but still allow the box to resonate.