It's conceivable that three Big12 teams could go 9-0 in league play (for example, CU, BYU, ISU all could have done that this year). Let's say the one that is left out of title game (purely by happenstance of the schedule they were assigned) also went 3-0 in OOC play and is therefore invited to the national playoff and wins said playoff.
In this scenario, the undefeated national champion never even had a chance to win its conference. That's ABSURD.
It doesn't matter how obscure a potential result is, if it's simultaneously mathematically possible and logically completely whack, you have a broken system that makes no sense.
One possible partial solution to this = get rid of the title game. With no divisions and a league this large, it serves no purpose anyway. In the above scenario, you simply have a three-way tie for first. Then the playoff MUST have a fair, clearly delineated path to inclusion for all conferences. Can't be some mystery council that just bestows honors by eye test. Must have some assigned number of berths per conference, per geographical region, or some unbiased computer ranking system, or whatever that makes the selections clear.