I think I understand what you're saying... but just to be clear... you are not suggesting that a 12-0 ND team would have been "ranked" 5th by the committee because they couldn't get a bye. Right?
You're saying what a lot here have implied... the committee goes freelance on their own criteria & sets rankings based on things like matchups, potential rematches, & political/monetary influences. None of that is part of the criteria. The criteria for the committee ranking 1-25 did not change when we went from 4 to 12 teams as far as I know.
Based on their final rankings a 4 team playoff would have been Oregon, UGA, OSU, & Penn St. They don't set their rankings based on byes & matchups. The field & bracket is set based on rankings AND the rule that top 4 conference champs get byes. Otherwise, the committee would have had Boise at #3 & ASU at a