I think Auburn would be the 4 seed, under that scenario
Wisconsin, as an undefeated B1G champion should be no worse than 3. If the committee can view losing to a 9-3 LSU and a 11-2 Clemson team as being a better resume than finishing undefeated in a P5 conference, then we need to scrap the system.
Truth is ... Under the former system, an undefeated Miami would play an undefeated Wisconsin for the title. Both teams would be 1 and 2, as the only undefeated P5 teams.
This CFP BS has screwed up the system. And it's changing the system from when "every game matters" to the garbage we have today, where people really see a 2-loss team being on par with a undefeated squad ( Wisconsin and Auburn). That wouldn't be the case this far into the season under the old system ... And I don't see that change as a good thing.