What happened with the Oxy/Linfield match should not have been a surprise. The handbook specifically deals with such situations. Here's a phrase that all should become familiar with "Geography trumps seeding". Texas teams have long known the meaning.
"Geography trumps seeding" changing the first-round matchup is one thing, one covered in the guidelines.
Importing a team as a #1 when an undefeated team with an acknowledged quality schedule already resides in that region is NOT covered in the guidelines, nor can I find justification for it.
If MUC and Cortland State are in the same regional bracket, should MUC be the #1 seed? Yes. They are the generally accepted top team in Division III. If MUC and Cortland State were in the same geographic evaluation region, there would be no objection from this corner. But they aren't.
Moving MUC out of the North avoids the conflict with NCC. But it creates a one with SUNY-Cortland. And having looked at NCC & Cortland's resumes, I don't see how one should be favord over the over.