That's the thing about the idiotic "ball if the pitcher takes too long" or "strike if the batter steps out of the box" rule proposals.
Game Seven, bottom of the ninth, tie score, bases loaded, full count. Do you really think the umpire is gonna decide the game by either calling a batter OUT because he steps out :or: calling "ball four" because the pitch clock got to 0:00? DON'T CHANGE THE ******* RULES.
Just fine the players (or the coaches or the teams) for clock violations. They already have a uniform police department that fines players for wearing the wrong socks or too much "awesome" on their cleats. Just create an "Office of the GameFlow" that fines anyone who slows a game down: a slow trot around the bases, a long delay followed by a "Nah, we won't challenge", a mound visit that lasts three minutes, a batter who steps out of the box after EVERY pitch, a pitcher who insists on getting new baseballs (one of my pet peeves). It won't change the RULES of the game, but the players/coaches will learn (through their wallets) how to play the game quicker.