You're missing something here. Imagine the play without the clock running out. He runs past the line of scrimmage, throws a pass for a TD. We mark off 5 yards and (if they don't gain a first down after enforcement) don't replay the down.
Since we can't end a period on a live ball foul (other than non-player), we have to have an untimed down. So B to keep the points off the board has to accept the penalty, but A gets an untimed down.
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