Your first two statements are contradictory. If you get the math then it should make sense that being favored in every game does NOT necessarily mean there is a > 50% chance to go undefeated.
According to the math, if a team has a 90% chance to win they will beat that team 9 out of 10 times. The extreme likelihood is they will beat that team on the day they face them as well as any other team they have a 90% chance to beat. However, if they play 10 such games in one season the math says they are supposed to lose one of those games which means they are highly unlikely to go undefeated. And that's just the scenario where we are 90% favorites against all opponents. Obviously, those odds get worse once you include games where we are only 60% or 70% favorites. This is why the same FPI predicts ND's record will be somewhere around 8-4 this year even though they have us as favorites in every singular game.
Having said that, whatever metrics ESPN puts into their FPI suck. Their FPI has always been ridiculous, so I think we will do much better than they think we will. Maybe we won't go undefeated but I don't see us losing more than 2 games.