It's kind of like the umpire who holds up a hand so the pitcher won't pitch, but thinks that he is keeping the ball live for a pick-off or something.
NOUMPERE - Can you explain how an ump should "control" the pitcher? I am not an ump but always assumed that when an ump was holding up the pitcher, that the ball was in fact live. A good scenario might be when the batter is "digging in" and the ump is sort of backed away from the plate. Batter may be doing the little "time" gesture with their back hand, but I never assumed that the batter was always automatically granted "time" when doing so. I guess I thought of it as relaxed action where the ump gave a sign to proceed so as to preclude a fast pitch scenario.