Well, let me offer a reason for scheduling the Dakota schools to play a non-conf game:
MONEY!
Like it or not, playing one of the Dakotas will draw a lot more fans of the visiting team as opposed to playing a team from the MAC.
If playing NoDak brings in an extra 3,000 to 5,000 fans as opposed to a generic non-conf opponent, that means more money for the U in tickets, parking, concessions, etc.
If the Gophers ever played NDSU, it would be a guaranteed sellout. (and if enough Gopher fans dumped their tickets, you could literally have more NDSU fans than Gopher fans at the game.)