Fan Theories 17

Zeno (a.k.a The Omni-King, Zenny, Zen-Oh) is the childlike ruler of all Twelve Universes in the Dragon Ball saga. He is also one of the oldest and most powerful character both in the franchise, and in genre fiction generally (after his doppelganger Future Zeno!). He has power seemingly equal to his childlike naivety about mortal life and existence in general. This could be a reflection of his power as no-one can get close to him and only the "lesser deities" even seem aware of his existence. But Zeno could equally be expressing a senility on a galactic scale considering his extreme age. He (actually is he a he?) could simply have forgotten everything he learned and no-one has actually dared to update or correct his information!

OK, so why are there only twenty-eight inhabited planets (in the seventh/Son Goku's Universe) but twelve universes in total? Are there actually a lot more universes but only eleven with intelligent life? Is there just the one universe or Cosmos but divided into twelve sectors (so to speak), or even just galaxies? And how can one character rule an entire Universe (or at least claim to)?

Because that son of a bitch does!
Frieza may claim to rule the seventh universe but he acts more like an interstellar real estate agent than any kind of ruler or regent. Anyway, twenty-eight planets barely divides at all between all the stars and galaxies in one universe! But there could be billions of planets with intelligent life on them, trillions more with animal life but only twenty-eight with any kind of developed, spacefaring culture indigenous to it. Frieza may not rule a or lay claim to any of these.  
Dragon Ball Super strongly implies parallel cultures and individuals so the different universes could be parallel realities so to speak. They could be "paralleling" (so to speak) only a small portion of the <real-actual-total> Universe. 
What this means in English is that every universe is actually the same apart from one specific sector/portion.
And when I mean the same I mean totally and completely identical down to literally the last particle! 
Totally indistinguishable from each other so, actually, for all intents and purposes (and as far as the gods are concerned) the universe/each universe is a smaller and specific volume of galaxies. I get that this ends up being as big a head-fuck as managing twelve actual Universes, but this ought to be consistent with the idea of parallel realities.    
I should add that Bulma refers to the seventh universe actually having a center and that Earth (or "Dragon World") is at its edge.