In both cases, the FDA was generally run and staffed by non-political people who were at least vaguely competent. I have plenty of issues with how the FDA operated, but it didn’t matter much who was president.
Today, most of the Cabinet positions are held by people who love to talk, who are generally extremely wealthy and/or well connected, and who are generally unqualified for their jobs. And, even more relevantly, they have been very heavily interfering in the operation of their respective departments.