Originally Posted by s0phr0syne
The extra player(s) were running off the field, that's why PM rushed the snap, essentially knowing it would be a free play.
(of course it took a challenge to confirm this)
So it fell into what enjolras described as being the rule: if the players are aware that they are on the field and thus trying to get off of it, the refs wait and allow the play to occur. If the D has 11+ players and don't seem to be aware of it, instead just lined up in formation that way, then they whistle the play dead.
It is sort of like the difference between being lined in the neutral zone (not blown dead) and unabated to the QB (blown dead). I would guess the rule change was meant to protect the offense.