I quick drew something to show some of my thoughts. in the 1. line you see how it is more natural to little things on top of big things, f.i. little bots on top of a walking platform. In the 2. line you see that it is easier for little stuff to hide behind big stuff then the othe way around. The 3. line is related to shooting and arcs from the front(a) a tank and a bot may have the same area to hit. But from top(b) that could be different. this all is related to some balancing stuff and also to interaction between units.
Obviously you're completely incorrect that small units look unnatural under big ones. Inverted pyramids are a core tenet of the strategic player!
