[AtlUmpSteve]

Your first question answers itself in the rule. All parties are required to be ready when they are required to be ready. If batter is ready at 9.9, and pitcher still waiting, pitcher has violated; period.

To your more general question, it is never treated as both penalized. Treat the same as if both step out without permission or time granted; tell both to get in and not get out without permission.

As to the described situation, I would always allow a bit of leeway on a new batter stepping in before the first pitch. If 12-13 seconds, so be it; but not 22-23. And not for subsequent pitches during the at-bat. Let her hear her walk-up, let her "groom" the dirt, take a few extra swings; within reason, and only to start the at-bat. Let the pitcher let her primp and preen. Then be precise with the between pitches timing.