The Wormhole wrote:
"Although I agree there is no reason to believe the original Enterprise 1701 was Starfleet's flagship, the term flagship does not just apply to ships carrying flag officers, even if that's where it originated."
There is no reason to believe the original USS Enterprise
was Starfleet's flagship considering hints that suggest this position had already been taken by the USS Lexington
a) it's commanded by Commodore Robert Wesley (and not just a captain like Kirk or Tracey)
b) the bridge command chair is noticably higher than on Enterprise, Exeter
c) the Lexington's
"flower" insignia is worn by most Starfleet personnel that does not serve on a specific starship.