According to the FIFA Laws of the Game, the referee is the one who decides which end to play the kicks towards. This is announced to the players before the coin is flipped. In other words, the coin toss only determines who goes first. If he is letting direction be a coin toss option for the winner, then he doesn't know the rules. And if the game is important enough to have kicks from the penalty mark, then a referee that doesn't know the rules shouldn't be working it.