I think there is another rule that might be helpful in this situation.
I don't remember the number but it says that if you record a score that is lower then your actual score you are disqualified, but if you record a score higher then your actual score you get that score. In competitive situations when there is no official present, I would think it would be best to give yourself the penalty, then before signing your card ask an official if possible before finalizing your card.

But I would definitely agree that putting and hitting the flag stick no matter where it was placed would be a penalty.