Even if Notre Dame was undefeated, and had the hardest strength of schedule, by NCAA rules, Notre Dame cannot be any higher than 5th in the playoffs.
You missed the point entirely. The fact that the NCAA rules guarantee the top four playoff positions to Power-5 (er, Power-4) conferences in no way affects whether Notre Dame might be considered a favorite for National Champion, other than allowing for one more opportunity to lose a game.
But since you bring it up: Suppose Indiana loses to Ohio State (or vice versa). Who could argue against the notion that losing to Ohio State should be much more forgivable than losing to Northern Illinois?