There is one way to solve this.
At the end of the season, force teams that finish in the Top 32, to play two games against other Top 32 teams, outside of their conference, in the following season. You could have a drawing to determine the opponents, the details can be worked out to make sure it’s fair, i.e., one team is from 1-16 and the other is from 17-32. Of course teams will change in strength from season to season with graduation, but does the Top 25 change all that much from year to year?
That would force Boise State and TCU to play two top-notch teams, and if they win both of their assigned games, then they deserve to be considered as legit.
Or more to the point, force top-notch teams to play Boise State.
Didn't TCU play a #5 team, and Boise State play a #10 team?
The problem isn't that BSU, etc., don't want to play "top-notch" teams, it's that "top-notch" teams generally refuse to play the likes of BSU.
Anyway, the vast majority of college football schedules are set years in advance, with very little room for scheduling opponents on a year's notice or less.
The real solution is to actually have a playoff system. Otherwise, no team outside the major conferences will ever get a shot, even if they are the best team in the country.