Call it illegal when it becomes illegal. If pitcher or batter stops their action, no matter, as the penalty remains in force (different than slow pitch, where batter wants the option to swing, and that takes off the enforcement).
The base award is just that; an award. Tell the runner to advance, announce the new count (the IP is a ball), and get ready to play. There is no need for a delay, since the judgment of an IP isn't subject to discussion. If asked, advise why you called it illegal, and move on.
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