F&A rates (facilities and administration, “indirects”) are subject to negotiation every 4 (IIRC) years, where those costs are accounted for (perhaps not well enough, but that is a separate point). The administrative component of F&A been capped at 26% for years and R1 universities are maxed out, so the negotiations are over the facilities component.

You can know what the research organization costs as a whole; and you can know what's "worth" charging to individual projects. The rest is indirect costs, which you can measure and use this data when negotiating indirect cost reimbursement with NSF or NIH.