I would have a huge problem with a very average Clemson team being the 3 seed. It gives a huge advantage to a team who has done nothing to deserve it. It also will encourage Clemson to continue to play a soft schedule.
Yea, the amount of control colleges have over their schedule probably make guaranteeing certain seeds to conference winners different than seeding by division winners in professional sports. Not sure if it’s a problem or not. The desire to keep a shot at an at large bid may encourage them to schedule good OOC games, or they might decide to go all cupcake to avoid wear and tear that hurts them in conference games. The possibility (likelihood?) of the latter probably makes it a bad idea.
I’d like to see some official cross conference matchups, sort of like the cross conference challenge weekends like in basketball, where the results could be used to decode seeding between conference champs and at large invites. So some sort of rotation where prior years sec and acc champions square off, big 10 and pax 10 champs square off, big 12 and best Non P5 conference champ square off, and rotate which conferences face off as you go down the seeds. Probably be a scheduling nightmare for the schools, but would be an awesome week of football and generate a lot of cool matchups.