Speaking NCAA: There really wouldn't be a way to enforce the DB PF against Green Bay without offsetting it against another dead ball PF / UNS foul.
Although I did hear a story once of a big time college R doing just that by accepting the first foul from a reporting official, announcing it and then accepting another foul from another reporting official and announcing that one.
I don't have enough juice to get away with something like that.
I think the UNS against SF was justified (and this is coming from a die hard Niner fan). Yes Matthews ran his mouth before the game and yes he hit Kaepernick late but that doesn't give them license to go running into the scrum and getting into his face.
I also think that maybe Matthews got away with throwing a punch that wasn't seen.