Except for rare instances where facts are not in dispute, the NCAA mostly relies on the member schools turning themselves in for infractions. Until there is a governing body that has real investigative power, that is how it will be. The conferences have become too strong and have the backing to stand up to the NCAA and not cooperate with investigations.
So yes, when schools do the work themselves, the NCAA will impose sanctions. When there is a smoking gun, they will be able to impose sanctions. But gone are the days when schools were afraid to not go along with investigations. They are protected by their conferences.
As far as ND having to vacate wins, I blame that on Jenkins and his minions. They were the ones who put that sanction on the table, and then were appalled when the NCAA accepted it. I think there will be a time soon that those vacated wins will be restored, either by the demise of the NCAA, or an administration at ND willing to stand up and say we are recognizing those wins and that's it.