They pay the ball handler to do it. Simple. As I understand it the home team controls the balls after they are inspected. They have ball boys of sorts that do it. The Bucs QB in the superbowl paid off one of the ball boys to scuff up the balls to make them easier to handle because he heard the superbowl balls are slick since they are brand new and no one gets to touch them before the game (except the ball boys).
Scuffing a ball is not against the rules. Never has been.
Michael Sam said the balls he inspected were fine.