According to Sagarin, Baylor is 8-1 against top 25, Notre Dame 10-3. That's not a big gap. He also has Baylor rated much higher.
Citing records against Top X teams is the kind of arbitrary nonsense that metrics like Sagarin and RPI are supposed to avoid. Who cares who has if one team has more wins against teams in the top 37, if the rating clearly has one team ranked higher anyway? Baylor is 20-1 against RPI top 100 teams, Notre Dame is 21-3. There's a number for anything if you choose the right cutoff. If RPI is the metric, then make Notre Dame a 1 seed, but give the same to Baylor. If it is not, and it is based on other metrics or "eye test", then give it to Baylor, because all agree Baylor is the better team.