There is a less than ten percent chance that Boise makes it in as a higher seed than the B12 champ, and that scenario would require the B12 champ having three losses.
The whole system is designed to favor the elites. We aren’t the “elite” of the elites, but we are definitely higher up the pecking order than Boise is so any two loss B12 champ is going to be ranked higher than a single loss Boise State. It just is what it is.