Colonels- I have not seen anything that would lead me to believe that prestige is a factor in the Proj Report. What I have seen is that the amount it values good wins (top 50, top 100 to lesser extent) is huge. Any wins over teams not in the top 100 aren't worth anything. Also, in that same light, losing to top 50 teams doesn't hurt you that much, losing to top 100 is a little knock, but not that huge, and losses to teams over 100 RPI knocks you quite a bit. To me, this system really makes sense. If you can beat tournament level teams, you get in, if you're losing to non-tournament teams, you won't make it.
I'm on my phone, so I can't look, but if you'd like to examine those 3 teams, I propose we post their records vs. those 3 subsets of teams.