If you win your conference of course you aren't the NC. After you win your conference in a non arbitrary way then you play in a tournament against the other conference winners to see who is really the best.

Even if the winner of conference X is not as good as the second place team from conference Y it doesn't matter, because the second place team from conference Y already lost to the best team from conference Y who is going to the playoff. If the winner of conference Y beats the winner of conference X then so be it. And if they lost so be it. It's fair and completely non arbitrary. The results are determined on the field.

In your scenario the judges of the beauty contest would say - well the first and second place teams from conference Y are better than the best team from X so they both "deserve" to be in the playoff and the best team from conference X gets to stay home. So the results are determined in a boardroom and not on the field. In what world is that better?

BYU may have been the top dog in the WAC in 84 but under the current system they probably would have been left out because of SOS. Does that seem fair or realistic? BYU, TCU, Boise and Utah have already been left out of a similar system because they didn't pass the smell test - forget about on field results. And all four teams could easily have been the best team in the country.