bad argument. suppose a champ has 2 or 3 losses and another much better conference has an unbeaten and a team with one loss ? that's fair ?
I assume you were asking if a 2nd place team in another league was better than another conference champion( you couldn't have an undefeated team that didn't win their conference championship). Secondly, if the intent of college football is to keep the playoff small then you should have to win your conference championship to get in. Again, your scenario is trying to draw us back into the picking and choosing and eyeball test.
Well first of all we don't really know who is better, the leagues don't play each other enough to really say which league is better except by observation/again more picking and choosing. Maybe one league is much deeper than the other league. Maybe one team that lost twice early has simply improved to the point where now they are the best team.
If you want a larger playoff 16 teams or more then sure there would be some choice made but if it is 4 or 6 it needs to just be conference champions. People play their way in from the P5 leagues and no human element to it that discriminates against certain teams.