Wow. It was because the Committee judged ND to be unequivocally better, not comparable to, the teams below it that it didn't go to the Protocol in deciding where to rank ND vis-a-vis those teams, while it could not agree that one of Oklahoma, Ohio State or Georgia was unequivocally better than the other:
There was little debate about Alabama, Clemson and Notre Dame. There was a lot of debate about Oklahoma, Georgia and Ohio State. The debate was deep, detailed, and occasionally contentious. There was division.
I can report to you that different people in the room made a case for a variety of different outcomes. I don't think we left any combination off the field.
Some committee members believed Georgia should be No. 4, some believed Ohio State should be No. 4. Some believed Ohio State should be No. 5. Boy, did we debate it. As we considered three teams for the No. 4 slot, the committee did not believe that any one team was unequivocally better than the next. That meant we went to our protocol.
The protocol are guidelines given to the committee by the commissioners when they created the playoff. It's our rules of the road. It includes a variety of factors that we use to judge teams. No one factor is more important than another, and this year, the difference among 4, 5 and 6 was very close.
....
"ROB MULLENS: Well, again, once we determined that -- as we were talking about those three teams being Oklahoma, Georgia and Ohio State, once we determined no one was unequivocally better, we go to the protocol, and the protocol has several factors, and conference championship is one of them. It's very important. When you look at the history of the playoffs, look at the number of conference champions that are in the playoff. It's a large percentage, so it carries plenty of weight. But there's other factors, strength of schedule, et cetera, and as we went on in this debate, that conference championship was a key piece for Oklahoma, and it did make a bit of a difference, but those teams were so tightly together, in the end the committee thought that that put Oklahoma at 4...."
The critical "lesson" we learn here that benefits ND is that, according to Mullens, "No one factor is more important than another," i.e., conference championship does not trump the tie-breaking factors.
Link: College Football Playoff Media Conference transcript