Yes. They may do that one day. But there is a reason ND has resisted joining a conference for oh...about 100 years. They don't want to join a conference. They like their niche. They like being able to schedule as they choose. We are only talking about this weird scenario that will never happen. In this weird scenario that will never happen...and you have to go back to the OP to understand it...there is an advantage to ND for playing an "independent championship game." It's the "independent championship game..."i.e., the 13th game which TCU and Baylor didn't play which was why they got left out. In this weird scenario that will never happen that was referenced in the OP, a championship game is the advantage to ND...so they are not at a disadvantage to teams that played a championship game.

Note the actual protocol the committee uses. See what number 1 is?

http://www.collegefootballplayoff.com/selection-committee-protocol

Principles. The committee will select the teams using a process that distinguishes among otherwise comparable teams by considering:

Conference championships won

Strength of schedule

Head-to-head competition

Comparative outcomes of common opponents (without incenting margin of victory)

Other relevant factors such as key injuries that may have affected a team’s performance during the season or likely will affect its postseason performance.

If that's not enough to convince you that in this ridiculous scenario that will never happen it would be an advantage...just listen to what the committee chair said.

http://collegefootballtalk.nbcsports.com/2015/04/25/jeff-long-says-13th-games-were-factor-for-cfb-playoff-committee/