Just some general observations: Any loose ball (kick, pass or fumble is NOT OOB until it TOUCHES something OOB, so there's no whistle until the kick comes down.
It's helpful, when the Umpire is able to refocus attention down field, when a kick passes by IF & WHEN the action in front of him doesn't require his continued attention, but when that focus can shift, depends on what action is actually going on during THAT play.
Responsibility to blow play dead, rests primarily with the wing official on the sideline the ball went OOB, after which ALL officials should both mirror the clock stopping and sound their whistles to insure play stops across the field. ANY official SEEING the ball touch down is authorized to stop the clock, but that is normally the closest official to the fact who initially responds.
Personal Contact fouls can occur while the play is unfolding (live ball foul) or after play has ended (dead ball foul). The Referee has authority to reverse a call, although as you describe this event, he was WRONG in doing so, for the reason stated. If the action itself was judged to merit a flag, depends entirely on the action, timing determines whether the foul is live ball or dead ball.
The Coach has a right to question the decision, but is required to do respectfully, and as indicated above a violation is either USC, or it is nothing, as determined by the R. A violation would NOT relate to a "sideline warning".
