Think of it this way: If you are using your regions officials then the coaches "scratches" come into play. Coach A has scratched the 1,3,5th ranked officials and Coach B has scratched 2,4,6th officials. Now you have your 7th,8th, 9th best offical working that championship game.
Also I am sure that a few years back two 11th region schools were scratching officials based on which ones the other team liked because they would likely play each other.
With out of region officials there is very little prior relationships and no scratches. Also much less of a chance of the official anticipating who is supposed to win.
Most officials and coaches I have spoken to don't hate it as much as this thread suggests.