The captain is most certainly in command of his/her aircraft. A smart captain will set a tone in the cockpit that will allow the maximum protection for his aircraft with the tools at his disposal. Getting sucked into a shallow debate about who has more stripes on their sleeve and who is playing second fiddle to whom, is not productive and may actually detract from security as well as safety. A captain who is willing to step back and allow his crew to do their job (FFDOs included) will in all likelihood be more successful and command more respect. Great captains don't have to tell anyone they are in charge, it's already known.
He's at the three point line.... SWOOSH!