...specifically the Praetor's flagship, the ship in the episode...
To be exact, the Praetor's
finest and
proudest flagship. No doubt he has a garage full of them, in all colors of the rainbow, even if some aren't as proud as the others.
In other words, no, this isn't a command vessel on which the Praetor flies his flag (he'd demand more headroom, I'm sure). But it is the pride of the fleet - or one of them at any rate - in the same way a specific ship or ships can be flagship to a cruise line.
And yeah, the Romulan mission seems to have been a single probing raid. But there's no telling whether it was part of a wider campaign or not. As Kirk holds back initially, the Romulan commander says that "studying the enemy for weaknesses" is what he himself would do. If this were his very mission to begin with, he'd probably phrase that a bit differently...
Since the Romulans are operating a WWII submarine here, it would be natural for them to operate like a WWII submarine does: sniping at targets of opportunity, at the skipper's discretion. The mission might have been a generic "Go out there and wreak havoc", assigned to dozens of ships simultaneously. Our commander just chose to be bolder than others, going against Earth military outposts, and paid the price.
Timo Saloniemi