Well, when Presidents are the ones making the decisions based on things like "like-minded" institutions and academics stats instead of win-loss records and past championships, then, yes, I can see an argument for UND-USD.
But, you make an interesting argument about how things change in sport. There again, though, at the time of the big Big Sky door slam, UND-USD were very competitive with the NDSUs-SDSUs of the world. So if athletic standing had even remotest bearing on getting in or not, then, UND-USD would have been on pretty good footing there, too.