Cox apparently confirmed that he thought he was winning, despite the coaches saying they were screaming that he was down (and the scoreboard showed the same).
Penalties have always out-ranked on mat action and the shot-clock IS a penalty. We can talk about the way its called and I'd largely agree (I have a theory I might write about after the Olympics as to why it appears so strange), but it is consistent with all the other rules.
Rules are arbitrary. ALL rules. These are made up competitions. Any change would be good in some ways and bad in others. Arguing that we don't like the rules because our guy didn't know them/understand how to win the match is just whining.