You'll call it a distinction without a difference but Minnesota's starters are overwhelmingly 3 and 4 stars. They do have a few 2 and below stars on Defense (one being Antwan Winfield Jr- but most will agree that he's just a little better than that).
You and the committee seem to by employing the intuitive "Alabama is better because of course they're better" approach. I'm not even saying you're wrong. Gun to the head, I'd pick Alabama in a head to head- but I'd have taken Penn State last week too. The problem (and why I think many are frustrated), is that the intuitive approach, while often correct, is difficult to defend. The committee can't say "well honestly, record be dammed, we think team A is just better, because, well, they just are." So they have to figure out how to justify it, which exposes/ creates the contradictions that people are bringing up now.
Ultimately, I don't think that the Alabama v Minnesota thing matters much. If MN wins out (highly doubtful), they're in.