BYU was 9-3 in 2015 while Boise State was 8-4 with a softer schedule.
You don't think that will matter for anything? How about this: BYU is #38 in the S&P+ rankings for 2015, while Boise State is #59.
I don't know how many starters Boise State returns in 2016, but BYU will return 7 of 11 on defense plus 9 of 11 on offense plus the punter. That's a much bigger group of returning starters than normal. I highly doubt Boise State returns more than that, but even if they do, they will start the year lower seeded than BYU by the computers that Vegas uses.