After a touchdown in football, who has the say on the offense: the coach, players, flip a coin?
Coaches tell their players in almost all cases to go for 1 or 2. However it is ultimately up to the players to run the play.
You do not tell the referee that you are going for 1 or 2. You do the action that gets you 1 or 2 points. So if a college team wants to go for 2 and not follow coaches orders, they can go out and run a play or a fake field goal try to gain 2 points. And the opposite is true too. A coach could send out 11 players and if they wanted to kick a field goal they can.
The coach has three powers to help him. He can call timeouts, he can order players off the field (if this happened said player would be ejected), and players would fear being cut by coach.