Billy, if you look at the tournament pairings for D3 this year, 5 of the 8 regionals are played at a host site where they have also placed the hosting college in that pool. Obviously gives the host team an unreasonable advantage, especially if they are #1 or #2 seed.
As for placement of CNU and SU in the same region, I don't think anybody can come up with a good reason to place the #1 and #4 team, both from the same conference, into the same region, so that one has to knock the other off to advance. I understand that there are geographical reasons to place teams nearby, but there is also latitude for logical placement of teams, which wasn't used in this instance. Totally absurd.