I recently reviewed a grant proposal for the USDA. We agree to keep this information confidential, yet the proposals and our review travel by university email. It would be easy to harvest the proposal and my evaluation using FOIA.
But the USDA makes me sign an agreement that I will keep the information confidential and cannot provide the information via FOIA. My institution didn't sign off on this, just me. Would the USDA, the researchers, and my private correspondence be protected? Probably not.
The USDA says that it is their job to determine if the materials are to be distributed. If the university receives a request, they don't reach out to those involved and ask for permission. They fill the request.
So if Karl Haro von Mogel asks me questions about the review, who's lab it was or what the project was about, I would have to decline providing any details.
But if he wants to see this confidential review, he can do the anonymous FOIA request to the university and get it.
Then he can admonish me publicly for not being transparent and then publish the content of a private document on the web.
There are times when academic researchers, striving for transparency, must heed confidentiality agreements in order for the process to work properly. Unfortunately (or fortunately if you like seeing private documents) the laws that ensure transparency are not compatible with the need to occasionally maintain confidentiality.