The penalty was applied in response to Tiger's remarks. The drops are observed by officials in the first place, and no infraction was noted. It would seem then that they took Tiger at his word that he had dropped illegally, and it is a mere footnote that ex post facto analysis showed that he hadn't actually done so.
Later on it was found out that a former rules official saw the bad drop on TV and called a rules official he knew at the Masters. It wasn't just Tiger's comment.