A season is longer than one game and the entire body of work needs to be considered, including SOS (NDSU > YSU), and we lost to WVU, and NDSU beat a team ranked higher (at the time) than WVU.
Based on all variables, in that scenario, I'd rank NDSU higher than YSU, but not by much.
As far as the money game, the FCS model is bizarre and needs to be abolished. The MVFC has no peers in the FCS and the FCS actually has a non-scholly and partial scholly conferences. The MVFC is ranked higher than multiple G5 conferences. There should be P5, G5 plus competitive full-63 scholly FCS conferences, and send the rest of the FCS to D2 or even D3. So, based on whacked division distinctions with D1, I wouldn't ban intra-D1 games because one is FCS and one is FBS.
In the post-Heacock era, we are competitive in these money games. I feel the BIG's FCS ban is because teams like ISUr and NDSU beat their teams and embarrass them.