What about being able to assign a ship(s) with flag bridge directly to a Naval Admin Command? Said ship would normally be kept at port or patrolling the local system and the NAC bonuses are applied normally to all other commands/ships below it.
If said ship leaves the system, the NAC bonus leaves with it, applying still only to those ships under its command. While the home system of the NAC loses the the bonuses while "The Flag is away", but the officer is still technically assigned the post so it doesn't get vacated and autopromoted into.
Flag bridges and officers in a regular old fleet would still function as they do currently. So you have your Commodore/Rear Admiral commanding individual squadrons while Vice Admiral So-n-So in the SS Big Bad and Scary overseeing the 1st expeditionary fleet command and on occasion goes on patrol when multiple squadrons are needed.
Edit: thinking about it, might want to also reduce the admin bonus while away from the home system. So that 1, encouraged to keep the officer in home port to get the full bonus and not just exploit it with just a single homeworld housing the entire Naval structure. And 2. Makes thematic sense, since the flag/ admin Commander wouldn't have their full staff and support network on board as opposed to being ashore
