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To me, this is not baseball. Timing rules are there to prevent the stepping out stepping in nonsense. I can't remember the last time I had someone stepping out after getting in ... it just doesn't happen anymore, at least locally.
But if it did, I'd remain ready for the pitch, and call the violation on the pitcher when it happens. If the batter stepped out and caused the violation, I'd call time, gently remind the batter that we don't do that, and move on.