It really makes no sense for overhead to be calculated at the university level, but it sounds like that's how it is done?

Sophisticated research into particle physics, material science, and (for the last several years) AI does come with significant overhead costs for opex. Sophisticated research into most of computer science, mathematics, and other theoretical scientific disciplines does not, let alone humanities research.

I think a large portion of the difference in overhead rates is due to the last item you are confident of in your list (i.e. Duke can tell NIH "if you want our world class researchers to work on this problem, here are our rates", and some random school cannot).