The status of the clock is determined by the results of the last play regardless of the penalty except for a delay of game or an inadvertant whistle.
In this case without the penalty there was a change of possession and the runner went out of bounds. The clock would be started on the snap.
The clock always stops to administer a penalty but the status of the clock is usually determined by the result of the down, even though, it may be replayed.
Might also note 3-4-3b,c state the clock will always start on the snap whenever B gains possession of the ball or either team following a legal kick.
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