Thanks for making my point for me. Who you beat/lose to does matter. While NU beat awful Georgetown and DePaul, Indiana lost to Top 10 Kansas and Arizona. They play NU's schedule and they likely have a better record.
They have most of the same good wins as NU (Purdue, MSU, Ohio State, Illinois, and Wisconsin) plus Rutgers, Michigan, and Xavier. The two wins over Indiana are more important if evaluating just the two teams, but they are by a total of three points. Michigan has beaten NU twice (and the games ultimately weren't particularly close), but I don't think anybody believes they should be ranked ahead of NU.
The committee is tasked with evaluating every team and their entire body of work. I suspect NU's weak non-con gave a still-gelling team much-needed confidence and that may ultimately have led to its B1G success, but the team didn't distinguish itself with its non-con play.