Not for leaving the box but for not stepping into the the box and bat. You call it a strike no matter what.And Give the extra Strike.
7-3-1 Penalty: For failure of the batter to be ready within 20 seconds after the ball has been returned to the pitcher, the umpire shall call a strike. If the batter leaves the batter's box, delays the game, and none of the above exceptions apply, the plate umpire shall charge a strike to the batter. The pitcher need not pitch, and the ball remains live.
So if the batter steps out with both feet, without being granted time by the umpire, and the umpire judges that the batter delays the game, he may issue a strike. If the pitcher also delivers the pitch, another strike shall be called no matter the location of the pitch.
You don't get 2 strikes on one pitch in 7-3-1. The "So ..." statement is Grayhawk's erroneous conclusion. Edited to add: The penalty strike referenced in 6-4-d-1 is from 7-3-1 so on furthor reflection Grayhawk is correct.
You get 2 strikes under 6-4-d-1. Situation b where the batter steps out with both feet and does not get time and the pitcher delivers a pitch. You get a penalty strike and an automatic strike on the pitch.
Most chapters I'm aware of encourage not seeing the second foot go out and just call 1 strike on the pitch. You will get enough flak on 1 strike when it's nowhere near the strike zone.