To be honest, I have no idea what you are getting at in this post. So I'll just address the first point. I do think undergrad matters, minimally though. You get a 4.0 at Rice and a 4.0 at a random small public school, Rice kid will win. But I think a 3.7 at Rice is no necessarily better than a 3.8 at the public school. It gets really difficult to decode stuff at this level, because if any bias exists, it mostly exists only in the mind of the person reading your app, not any official policy. And then, don't forget that one of goal of schools is to get a high average entering GPA. The 3.8 obviously wins.
That being said, I strongly believe that most of any bias, if any, is simply due to the fact that the better/best student TEND to attend the prestigious universities. You take a spectacular student and you put him/her in any university, and they'll do well. But they tend to attend these more prestigious ones, because why not? That's why schools like Harvard have grade creep and grade inflation. I just think that the students that go there are all A students. Hence, high GPA, hence interviews.