In a region based system using your method, 5 of the best teams in the country might be from the same region (SEC) in a particular year but are capped at 2 teams
This is just the opposite side of a bad fence that AQs creates... neither AQs or Caps have any place in a playoff meant to determine the best in the Nation. The real, real, really real answer is that Conference finishes should be related to what they really amount to, bragging rights.
Come up with a legitimate comprehensive ranking system (committee, BCS, metric, whatevs) and put the Top 16 in straight, in that order, no byes, no AQs, no Caps, Top 3 pick which bracket they host with #4 getting the remaining bracket, first round on college campuses, remaining rounds use major bowls. The end.