Admiral Pertrarch DOESN't always give the orders
His orders come from the GTVA Security Council
In reality, who you see as Command isn't *really* Command. You can attribute the in-game role of "Command", the black guy with the oversized head set as somethign equivalent to a Fighter Controller or Airborne tactician of today's Air Forces. But he would operate from GTVA 4th Fleet HQ or whatever, the GTVA's COMMAND staff in that system, therefore his messages would be coming from Command. As far as we know, and what I think, is that black guy whom we call "Command" could really only be a Lieutenant or a Captain, but HIS orders come from 4th Fleet HQ, whose orders come from the GTVA Security Council. The 4th Fleet HQ/Command relays orders down the chain to Admirals, who relay them to their Squadron Leaders, who relay them to their pilots who follow these orders. When in mission the squadron/flight leaders are put in direct contact with 4th Fleet HQ/Command and so on etc.
That's my understanding. You've given me a reason to make a flow chart of the GTVA Command Structure.