Kira commanding it makes no sense whatsoever, it's a starfleet vessel and she's not starfleet.
How would this be different from Sisko commanding a space station that is actually Bajoran property? Sisko is not Bajoran. He has had no training in the Bajoran militia, or in the Bajoran military forces preceding the occupation (if there were any; we never hear of Bajorans of former warrior caste identity, but it could be Cardassians killed all of those early on). He holds no Bajoran rank (not even an honorary one) and wears no Bajoran uniform. Yet he commands this space station whose technical specs are largely unknown to him.