Option 1: Kyle Whittingham retires, Scalley takes over as the Utah HC and hires Jay Hill away as the Utah DC - numerous top defensive BYU players and recruits transfer.
Option 2: Utah wins the conference, getting the auto bye and the #3 seed. They then beat the #6/#11 winner (let's say Oregon vs Clemson) to make the national semifinal, where they lose a close game to Ohio St. Ohio St goes on to beat Georgia in the championship game.
Obviously neither is great, but that's the whole idea of "would you rather", having to decide between two unappealing scenarios
FWIW, I agree - Option 2 would be notably worse for BYU