Kansas, Kansas St. loses to Iowa St., Iowa St. loses to Utah, and West Virginia wins out beats BYU in the conference championship game, it's very likely that both Boise St. and Army finish ranked ahead of B12 champion West Virginia.
Technically it's possible, and none of those results in and of themselves is so improbable that you would say they won't happen in isolation, but the odds of ALL of that happening is almost 0. And yes, I know that we don't need quite that amount of chaos for the B12 champ to miss out, but it would require multiple upsets by multiple teams in order for it to happen so I wouldn't really fret about it when the probably is very far from happening at this point.