Honestly, I think the Committee is going to have to relook their seeding criteria.
Byes for conference champions is a dumb idea, especially when a Clemson wins the ACC.
"Not holding the conference championship game loss against the runners-up" is also dumb. If a 12-0 team playes an 8-4 team in the conference championship game, and the 8-4 team wins somehow, that does not mean the 8-4 teams should be in and get a first-round bye. That's dumb.
The committee should probably just rank NCAA Div 1A teams 1-25, and include 1-12 whether they win the championship game or not. Yeah, take the win (or loss into account), but do not automatically seed conference championship game winners anywhere. Just rank the teams. 1-4 get a bye wherever they are from and whether the won the conference championship game or not, 5 plays 12, 6 plays 11, 7 plays 10, etc.
And for the regular season, the committee should pay close attention to strength of schedule. being 12-0 and playing the 120th strongest schedule means little (unless we want games like Clemson-Georgia or Ohio State-Texas disappear from the regular season; if we want to see 12 weeks of Bama vs UT Martin and Ohio State vs Ball State, then go ahead and ignore strength of schedule)
When I am Planetary Commander (hope you'll vote for me!) that what I will do.