Let's use your analogy with Navy, Upstream. You've been refuted with JHU, most would agree. We have a stronger SoS than Navy, so we should be in before them right?
If it were up to me, I'd put Rutgers in before Navy.
But you're still missing the point. You can't look at only one factor, whether that factor is W-L, H2H results, SOS, or common teams played. You have to look at the entirety of all factors on the resume. Right now SOS is Rutgers' weakest factor.
Ideally I want both Hopkins and Rutgers to make it. But I expect that only one will. I don't know which one will make it ahead of the other. Both teams have resume weaknesses that make it a close call.