I see your points. Ideally speaking, this suggestion wouldn't change the game for anyone who is happy with the current Rank requirements. Meaning, you wouldn't have to use it. You wouldn't have to opt-out. Your game will still require a superior officer to be in charge of every level of your command structure.
Ideally speaking, this suggestion would provide greater control of the command structure for those who want it. It would be an opt-in mechanic. Possibly through Space Master, or just a setting under the Fleet Organization window.
Additionally, I don't see this as a niche request. Almost every facet of Aurora seems to include a very high level of control for the player. From the size and function of a ship, to the strength and outfitting of even the smallest ground unit, to the name and company of a single component. It goes on. I would say, the ability to tailor your empire, federation, or republic, to your whim, is at the very heart of Aurora.
Then again, I am incredibly biased when it comes to this suggestion, so I could be mistaken.