If his power doesn't work with a BC on board, the BC can give him another activation but to no avail. As far as I can tell, that addresses your original concern exactly? I also figured - there's only one person in command of a ship. You can't have a captain and an admiral shouting out orders.
The way it's worded now, the target of the SA's ability is the one that can't have a BC on board. A ship with both an SA and a BC can still give out two AP boosts, it's just neither of them can be on the ship that the SA and BC are both on.
Also, another thing - it might be worth reducing the AP cost of shields a bit, now that each shield activation only protects one arc, not all four arcs.