In Naval sense an Admiral (of any rank) really isn't in command of the ship. The Admiral's job is strategy, planning, etc. He gives the generalized directions and leaves it to other officers to figure out how to make it happen.
An Admiral with a number of ships at his command can choose to have his offices, his "flag", on any of them. This ship becomes the flagship. The Admiral doesn't displace the commanding officer of the flagship, though he is higher in rank. The CO of the flagship becomes a Flag Captain and generally still carries out everyday command of the vessel.
So all in all yes, we should have the ability to promote BOffs to Captain. I am hoping that whenever the full Admiral rank is available promoting BOffs to Captain will be available as well.
Yeah, but this is space in a new era where some of the old foundations of the miltary are out and a new one is in. In this era, you get to command your ship if you want, and set the uniform codes yourself. I do agree with promoting one first officer to Captain as long as we get to use captain skill slots on your ship, no matter what class.
What I really want is to use the higher skill slots of my BOFFs on any ship I command. Just because I fly a cruiser doesn't mean I should get stuck with using only LT or En slots for my tac officers. There is enough room on the screen for me to use all my BOFFs' abilities.