I think you're failing to see something here. First of all, since the B1G sent two teams to the playoffs, all of their remaining teams had to play up on their bowl allotment schedule by two teams. Instead of Purdue playing against LSU, it would have probably been Michigan, Ohio State, or Penn State. Same is true throughout the B1G scheduling of bowl games. Despite all of that, they still went 5-4 in bowl games.
As for Purdue, they didn't stand a chance, since their offense took a major hit with their quarterback, star receiver, and starting tight end all sat out the game, as well as multiple other players. Purdue would have gotten beat up even if those players played. Purdue lost five games, you know.
This will all be remedied after one more year of a four team playoff. Once 12 teams are in the field, chances are strong that at least 8 of them will be amongst the best 12 teams in the country.
In today's environment, you really can't take away much from conference records in bowl games, due to all the players opting out. Alabama players chose to play, and Kansas State was the recipient of that ass whopping due to that. Was Alabama one of the best four teams? Maybe, but being in the best conference in all of football sometimes hurts you when you lose a couple games, despite losing them both on the final play. Would Alabama have been favored if they played TCU, Michigan, or Ohio State, had they gotten in? Probably, but college football is a complete mess right now, and will only get worse as years pass.