Rule states is penalty during play in which you have a inadvertent whistle takes precedence and will be administered is accepted. The covering official throws the flag and blows his whistle right after thinking play was dead would the rule still apply?
Yes. The foul happened the instant before he blew his whistle. It did not happen after the whistle.
One of the most common is new guys will blow dead an illegal formation or illegal shift.
If they do it before the snap, we can wave it off and reload.
If they snap the ball, then the whistle is blown, we can enforce it, since the foul occurred the instant the legal snap happened and the play was killed inadvertently immediately after.