I, personally, would err on the side of preventative officiating in most cases. If the 12th player is heading off, I'll give him the opportunity even if it's after the "3 seconds". If there's 12 in formation and nobody seems to notice or care, then I'll probably say something ("Count your players!") and flag if there's no reaction. The offense would get a shorter leash than the defense.
To wit, I'd flag situation 1 the fastest, 3 the second fastest, and I'd have to see if 2/4 could rectify the situation before the snap, potentially making it a live ball foul rather than killing it pre-snap.
All of those situations are fouls by rule, but it does nobody any favors to flag them all.