AFAIK, the other hospitals/clinics under the Northwestern umbrella don't really factor into whether the downtown Northwestern Memorial campus qualifies for 340B (insofar as they all have their own CCNs and qualify independently). In this case, Northwestern Memorial qualifies because it a) got reclassified as rural b) became an RRC (likely based on its staff specialty mix) c) meets the RRC DSH threshold of >= 8%.
Northwestern Memorial does treat a lot of rural patients, so maybe it does deserve 340B. That said, it seems clear that it's not they type of struggling safety-net/rural hospital 340B was originally intended to subsidize.