First thought...how would you ever have a player thrown out when the ball is held? By definition, if the ball is held there will never be an out.
Second, as to the original post, if the scorer deems the batter took third on the throw, rather than on the batted ball, then it would be a double and an extra base on the throw as noted. I would like to see more outs on those though...the batter is always safe.
(Note: I play in Modern 2D w/o animations.)