tl;dr The system is starting to work as intended, which is that you won't get every Prestige Point possible. And it will only work if people run as written.
Which apparently led to a *bunch of questioning* at GenCon during one of the specials because not enough of the tables did the secondary success condition.
So it does happen even during specials.
Actually, come to think of it, if there's a scenario that some of the players have GM'd before, and they deliberately *tank* the secondary mission objective or the GM de-emphasizes it so the table doesn't know it's an option and therefore is 'invisible' to the players, should the players who haven't played it before be punished for that?
** spoiler omitted **
Does the player tank it because they've run it, or because it's in-character for them to do so?