The evolution of football’s clockwork often takes strange twists and turns, cobbling together rules and necessities on the fly and then fixing things whenever they become problematic; a legacy born of the sport’s close allegiance to broadcast.
For example: 70 years ago, NFL referees used to salute towards the broadcast booth during football games.
However, the officials were not paying respects to the play-by-play guy. They were instead indicating that a player on the field had committed unnecessary roughness.
The gesture being associated with the penalty is not unique to football. In fact, it is still used in lacrosse, also to signal unnecessary roughness.