In Star Trek Wrath of Khan Kirk was a Admiral, Spock was a captain on the same ship Kirk Commanded the Vessel and Spock was First officer. What i like to see in STO. is the same if you are a Vice Admiral that you can Promote 1 BOFF to Captain and that the one is Captain is also the First Officer on that ship. Just like the Captain is commanding the ship and the Commander is a First Officer.
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.
Well then it time for Cryptic to introduce the Captains captain for every aspiring Admiral.
Somebody confident and oddly trained in that extra rank 4 ability to manage the day to day operation of your pride and joy vessel of the moment.
Very important for those awesome social opportunities to tell all in the bar the joys of being an Admiral and the luxury of choosing your on flagship.
Immersion may be missing we never knew existed before, start wanting now before its too late. ::p