Gotcha. Just trying to figure out why the coaches were ok with what happened in scenario 2.
Hard to say...perhaps the batter was a weak batter and was likely to make an out anyway. As an offensive coach, I am OK with this, given the fact that the umpire screwed up and advanced my runners.
In scenario #2....the offensive coach still has the option of taking the result of the play or the penalty for the illegal pitch.
Play - Batter out, runners stay at second and third.
Penalty - Batter returns to bat, a ball is added to the count, runners advance one base.
It makes more sense to me to take the penalty, but I'm not a coach.