Re: WTH is the NCC1701-D "the Flagship"?
One other thing to consider, the meanings of words change overtime. So today as stated above flagship can refer to the pre-eminant thing. i.e Flagship stoire. Who knows by the 24th century this meaning could have become the primary meaning of the word.
On the continent of wild endeavour in the mountains of solace and solitude there stood the citadel of the time lords, the oldest and most mighty race in the universe looking down on the galaxies below sworn never to interfere only to watch.