I think leaders should start as they are, and at game start, no commanders. That is, all Commanders should be gained through tech research, as unique civ heroes (unlocked by a tech) or as religion-based Commanders.
From a thematic level, I think at the start of a civilization, your nation is just too small to have so many chiefs, as it were. But once you start growing, you start to recruit Commanders to flesh out your leadership structure.