Because it doesn't "stop" the clock permanently, like a time out. The chains move and the ref sets the ball in play, and then starts the clock. You have to spike it or run a play. The clock will start regardless of whether the offense is ready to run a play or not...but it doesn't run until the chains are set. That rule was changed a few years ago.
Maybe I'm wrong about that, but I thought they changed two rules regarding the clock in the final two minutes, and that was one of them; the other involves stopping the clock on an out of bounds play--I don't fully understand that rule, but I thought the clock stopped out of bounds, and then the clock resumed once the ball was put back into play.