I think they could still get in as an at large. It would take a pretty fun scenario.

Oregon, Texas, BYU, and Miami win out and all win their conference championship games. Army beats Notre Dame, Navy, and Tulane and wins the AAC championship at 13-0 and leap frogs Boise State. In THAT scenario, a #12 Boise State would make the CFP as an at large bid, despite also being the 12-1 MWC champion.

(1)Oregonp[B1G]
(2)Texas[SEC]
(3)BYU[B12]
(4)Miami[ACC]
(5)Ohio State[at large]
(6)Penn State[at large]
(7)Tennessee[at large]
(8)Alabama[at large]
(9)Ole Miss[at large]
(10)Indiana[at large]
(11)Army[AAC]
(12)Boise State[at large]