They had refered to it as the flagship well before Chain of Command. In Sarek for example, I believe (I just saw it during that Christmas marathon).Well, they cast Alan Ruck for a reason -- they wanted someone with an aura of vulnerability and goofiness to play a newbie captain as a straw man to make Kirk look even better than if he had to deal with an experienced captain. The role in many ways is similar to the roles Ruck played on Ferris Buehler's Day Off and Spin City. Kind of silly, but hey, it was GEN!
As for whether Enterprise-B was the flagship, probably not. I actually like the idea of a Starfleet flagship, started in TNG. But I think that was still a mostly ceremonial title. To digress, the only time we see that Enterprise-D has some kind of official "flagship" role was in Chain of Command, where it's revealed the D would be the command ship for that sector if Minos Korva was attacked by the Cardassians.
Red Ranger
While it's true Enterprise-D was referred to as a "flagship" before Chain of Command, I thought I made clear the distinction. When they said "flagship," I believe it wasn't in a literal sense. In that ep, they call it the "command ship for the sector encompassing Minos Korva," but Jellico and the rest of the crew don't mention the work "flagship." So maybe they do use that term, but as others have pointed out, it's not a literal definition. The words "command ship" are a literal phrase. -- RR