# of combined Final Four appearances by EVERY MW team EVER = 9 (of which BYU contributes zero)
# of Final Four appearances by Duke = 15
Duke & BYU are both having great years and are both very talented. If being ranked #1 in the nation is a representation of being the most likely team to win the national championship, I think it makes sense why Duke would be ranked over BYU given the above stats (and the fact their records and SOS aren't *that* different).
In the end, it's just really difficult to compare teams in two different conferences who don't play one single opponent in common.