It would depend on how you explained the situation to the defense. Accepting or declining the penalty will not affect the Referee decision to invoke 3.6.3. The clock should still be started on the ready.
Like you said, acceptance of the penalty would not be a good choice for the defense.
It was not a legal way to stop the clock, so there should not have been any question as what to do. Whoever suggested it might be a legal way done incorrectly must be a lawyer or something.
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