I don't know ... I understand what you are saying, but I think it is harder to change when it is chalk to the rankings (1 v 8 v 9 v 16). Maybe not harder to change, but more easily justified?
This is the problem with the "neutral site" system that is currently in place. If the desire is to have the #1 overall seed to have the advantage, play the games in a system where higher seeds host games on campus. Until they are willing to do that, I don't think there should be any consideration to "protecting" the seeds.