As far as the line-up I would have had it fixed at the plate meeting. I know of no penalty just a question. "Coach i think it's going to be crowded in RF tonight."

On the throw to third if the catcher catches the ball the batter can stay where he is. You can't expect him to move out of the way in the instant between catching and throwing. If it's a passed ball or muffed catch then the batter has to vacate any area needed to make the play. Remember that it's intentional interference on a thrown ball.