I'll offer a guess. Equipment racks dictate a certain width (~17"), so that dimension is fixed. The I/O on the back needs a certain amount of space, which drove the height (keeping in mind that they wanted to isolate the power supply, so they had to stop the "wall of I/O" at the barrier between the power supply and the unit's brains). The depth was likely determined in part by the size of the main circuit board -- it would seem preferable to keep everything possible on that one board that fills the bottom of most of the unit. The excess volume that ends up empty is sort of a direct result of that, and I don't know for sure but I think it may even be useful to have that air there to provide better ventilation to the components for cooling.
Of course, all of this may be my inherent desire to always have extra space in equipment (or, in my case, equipment rooms...). The need to squeeze components into a small space can produce some ingenious engineering, but usually it just ends up being ingenious compromises. Hullguy's done commercial construction -- I bet he's seen some mechanical or electrical rooms that should have been 50% larger.
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Gonk