A lot of conferences have unbalanced divisions. As a 5 seed, they'd be playing the 12 seed instead of a conference title. That's likely a worse team than most of the formerly known as P5 teams had to play in their title game. It's fair, even if they are ranked 1 or 2, because it's the 13th game. It's actually easier than if they were in the current SEC or even BIG conference.
Seeding is more of a worry in R2. They would have to play a tougher 2nd round game than if they were in a conference. Regardless, they have to win 3 post-season games for a title, just like everyone else.