to be fair Mike, before Michigan State and Florida State last year, the last time a team in a power conference went undefeated in conference play (aside from teams on probation) was 2010. That is a two year gap with no teams. This year there were two teams as well. It isn't near as frequent as you make it seem. That is where the non-con comes in.
This year Alabama's victory over West Virginia didn't matter because the SEC West is so good and Alabama has the history and sway. I don't think Oregon's victory over Michigan State is the reason Oregon is in either, though it might be part of the reason they are at 2 ahead of Florida State. I do however think that if Baylor had a victory over a team like Mississippi State, Arizona, Georgia Tech, Missouri, etc. it would be in the playoffs ahead of Ohio State. That one victory would have made a huge difference for Baylor.