No World Champion or Grandmaster has organized this many events. I have organized everything from Scholastic events to major Open Swiss and World Class Round Robin tournaments.
Speaking as a prolific organizer, I have faced many “unusual” situations, including dress code. What I have done is simple. I waited until after the game / event (depend on if it was a 1 round per day or 1 day tournament, etc.) is over then I ask that particular player not to wear a particular outfit (or types of clothes) for the next round or in the future. But as a former World Class Professional Player, I would not want any arbiter / organizer to interrupt my focus before an important game. They can do it after.
In this case, even though I find the rules ambiguous, I am not disputing it. My argument is if the organizers and arbiters allowed GM Anton Kovalyov to play 4 games (2 games in round 1 and 2 games in round 2), what changed? Was this mentioned during the players’ meeting? Was this ever mentioned to him? He said no.
The organizers and arbiters could have told GM Kovalyov not to come to game 2 of round 1 with this type of dressed shorts. He would have no problem going to the store to buy some pants. So if they “only” noticed his shorts in round 3 (which is peculiar since he played Anand and round 2 and there were plenty of pictures taken with this shorts), the right course of action would have been to politely ask him to change to pants for game 2.
This incident was unnecessary. It is not good for the sponsors, organizers, FIDE, or chess in general.