If BYU has ability to attract better non-conference opponents than Boise St. does, that would still be the case even if BYU were in the MWC.
So the best comparison is BYU now to BYU back when it was in the MWC.
In 2003, BYU played 7 MWC games and 5 non-conference games of Georgia Tech, Stanford, USC, Notre Dame, and Boise St.
In 2004, BYU played 7 MWC games and 4 non-conference games of Stanford, USC, Notre Dame, and Boise St.
So those 2 seasons, BYU's schedules were about as good as BYU's schedule is this year.
In other words, if BYU were in the MWC and scheduled all 4 non-conference games with top-flight games (no FCS teams), its not that much worse than being independent.
So independent usually results in better schedules, but in its worse years the independent schedules are no better than the best years of MWC schedules.