The only spot in the rulebook I found is this: "The following two paragraphs are additional material for Rule 6.02(b) Comment, for Major League play only:
If pitcher delays once the batter is in his box and the umpire feels that the delay is not justified he may allow the batter to step out of the box momentarily.
If after the pitcher starts his windup or comes to a “set position” with a runner on, he does not go through with his pitch because the batter has stepped out of the box, it shall not be called a balk. Both the pitcher and batter have violated a rule and the umpire shall call time and both the batter and pitcher start over from “scratch.”"

It refers specifically to Major League play only. Is there somewhere else in the rulebook that covers all baseball??

That covers your baseball: it's excluding MiLB, which has its own rule.

The paragraphs were added to distinguish Major League rules (which is what our modified OBR games are all based upon) from National Association specific games, which have their own special rule where an automatic strike is called without a pitch being necessary.

Thanks for the clarification guys.