EEEEEEEEEEK!!! 
On the topic of admirals and squadrons, I will just say that part of the reason we historically saw the rear, vice, and full admiral commanding distinct squadrons was because these squadrons were separated in space and, for much of history, time (as far as communications go). In Aurora, fleets are usually all in the same place and communication, thus command & control, is effectively instantaneous, so there is less need to distribute valuable admirals across the actual fleet.
So I think the current mechanic works fine. The motivation for the Flag Bridge change was because the old mechanic was nearly useless, partially because the Reaction bonus was usually superfluous and partially because it didn’t give any bonuses for, e.g., detached squadrons or fighter wings. The new mechanic solves those problems.