one thing is MSM is already two games into the post season, which cornfused may have missed, so part of their 35 RPI is 2-0 in the PI vs top 100 RPI teams, which would make them 9-6 vs all other teams.
They also went 0-5 vs top 10 to 28 teams & 1-1 vs 62 RPI and 2-0 vs 90 RPI, while the second best team Messiah played was a 74 RPI team and they were 4-2 vs teams in the 70's thru 90's.
I would not have looked at margin of win until you asked, but my first impression was not much difference, until I looked at the games vs bad teams, in which case Messiah really romped on people, then I noticed they FCP'd, which will tend to stomp bad competition.
Overall, in this example, my gut says RPI seems to have it just about right, or as right as anything.
A formula that I used to use, was (RPI + Rank)/2, so a 12th ranked team with a 4 rpi would be the 8th best team in the country. A 25 th ranked team with a 50 RPI would be the 37th or 38th best team in the country. It is a second set of eye, maybe you do something like that already????