I really think you are putting too much stock in conference championships. The championship game of each conference is often a crappy game like ACC last year Clemson v Pittsburgh I think it was, or Big 10 Ohio v Northwestern. I don't know how long each conference has had a championship game but as far as the committee is concerned they are just a 13th reference point.
In this case you are right though Oregon or Iowa should get in but then again Oregon with that loss to Auburn - yikes. How do you leave LSU out when they beat Bama and only lost to Georgia while Oregon's best victory was Iowa and then nobody.
It depends on the circumstance of the conference championship game as you say.
In this scenario (assuming both Oregona and Utah take care of business over the next two weeks) you will have at minimum a 5v6 conference championship game which I am pretty sure is unheard of and they could be ranked even higher if one of the others slips up.
The Oregon loss to Auburn doesn't look great but it was week 1 at a neutral venue and they lost in the last play of the game. It would be harsh for LSU to miss out with their only loss against Georgia but more recent form should be taken in to account and they would have just loss to a team that made the playoffs so there is a strong argument they are incapable of winning the playoff. Oregon or Utah would be on a 12 match winning streak and woud deserve the opportunity IMO.
Hopefully LSU go undefeated and the PAC-12 winner is just an automatic in.
There still could be a huge shake up yet to come IMO with OSU having a tremendously hard shcedule to come. They have to play number 9 Penn State and then @ 15 Michigan and then a BIG10 championship game against top 10 ranked Minnesota or Wisconsin. They are a big chance to lose one of them and if they don't they should be ranked 1 at the end of the regular season. If they do lose one of those then that would bring Oklahoma in to the debate assuming they win the BIG-12
