It's worth pointing out that even football referees have a good amount of discretion when making a call. They don't change the rules, but they selectively apply them.
You might be right, but I think your claim is more controversial than you imply. For the most part, I think the league would prefer the rules be applied mechanically. The one exception I can imagine is giving a player a warning about borderline instances of some infraction before calling a penalty.
You can call holding multiple places on the field every single play. If they did that, the game would be ridiculous and nobody would want to watch or play. So they exercise discretion and only apply the penalty when the holding affected the play.
