I always figured the Black Flame operated so covertly that it's not really considered anything but a folk tale. It's sort of like you listening to a ghost story or watching some movie about possession. Odds are you don't believe in ghosts or demons yourself, so if someone walked up to you and claimed to "have had an encounter," how seriously would you take that?
That said, your point about magic can also be confronted with the Black Flame also being a supernatural entity. Maybe you can't actually scry for it? Maybe you cannot divine it? If it has any form of omniscience (and it could, it's a god-like creature after all,) then this wouldn't be all that far fetched.
I think the point is to create a more "lasting" antagonist. Judging from black flame players I've encountered, they tend to be more complicated than your average character, and frequently their nefarious actions, intentionally or no, are veiled as being something not attached to the Flame. Of course you have the random person that tries to pull some crazy ass bombing or something and write FROM THE BLACK FLAME in big bloody letters on the wall somewhere, but again, as per the first paragraph, odds are you'd think that person was a nutter.
I never played a black flame member, but I do know there's a hidden library somewhere in game with information about it. Who knows, maybe there's a reason lore-wise.
Just some thoughts.