The same is probably true of "finest flagship of the Praetor" in the TOS episode "Balance of Terror": not a formation leader, not a vessel hosting a flag officer, but simply the most presentable vessel of the lot. A bit like HMS Hood
was the flagship of the WWII Royal Navy in the sense of being the biggest (well, longest), the most famous, and the one whose loss mattered the most.
In turn, there have been several occasions where the word "flagship" has been used in the military context, and quite correctly. Say, Admiral Nechayev used the Gorkon
as her flagship in "Descent". It's just that no Enterprise
has ever received that treatment.