I am not going to speak in hypotheticals cause this thread is too specific.
However, from everything I have heard going back to even before this playoff officially started the committee wanted to give Conference champions priority over Non -conference champions. It all stemmed from when the SEC had LSU play Bama in the Championship a few years back with many people being angry about that result.
It got to the point that the head of the playoff committee was asked about this very scenario prior to the 2014 season and he something vaguely indicating Conference Championships would be prioritized in determining the Final four teams.
I think that when push comes to shove we will have 4 of the 5 Conference Champions represented (Unless Houston is Ranked ahead, which would make it 3 of the 5 Major conferences.)