12 men in the huddle is different, because it can create confusion and it does affect the play.you are frustrated with the flags/breaks in the game it seems. nothing is wrong with enforcing 11 men in the huddle as it affects the play.
in the scenario youre talking about, the 12 men penalty will only get called if the ball is snapped. if the qb can identify that and snap the ball ASAP without huddling thats just good awareness.
sorry, the 12 men penalty in your scenario is all about discipline on your subs.