As someone who doesn't follow the NFL I am surprised that they allow the teams to supply their own balls. Seems it would be less complicated and achieve an even playing field if everyone had to use the same balls supplied by the league. Does this happen in baseball/ basketball as well? From an Australian perspective it seems unusual.
I doubt this happens in basketball because the same ball is being handled by numerous people on both teams, so it wouldn't be fair to let one player or team break the ball in to their own preferences. The same would be true of your AFL. In the NFL, teams are using their own broken in balls, and the quarterback is (usually) the only guy who has to actually throw it.
Baseballs only last a couple of pitches and offense/defense are completely different games, so I seriously doubt anyone is allowed to do anything to any ball before the game. When a pitcher gets a new ball it is already pre-rubbed in a special mud, and they can rub it in dirt a bit but they can't put anything that will stick to the ball on it as it gives the pitcher an advantage.