Sometimes it is going to happen that the two best teams at the end of the season are from the same conference. And it is even possible that they won't have played each other yet. Sure, the second-ranked team should be conference champ if the top-ranked team is from a different conference, but not necessarily otherwise.
I know.
However, it should be a requirement to win your conference.
If it isn't a requirement to do so, they need to institute a 4 team playoff.