I think the TG commander should stay with it, but they should be able to fly from it. That way they can control what is needed and help with the fight. So if they stay in the tower, gun, PT or plane, all connected to the CV. If they move to another base, the command is given up.
Imo this would help a lot. If you limit them to a gun or the tower only, no one would want to command them! There are no points/perks that way.