I know more about the brain than I do about physics, but I would hope that quite a lot is gained from taking the laws of physics as a starting point.
The fact that the FEP applies to both humans and bacteria (and non-living things like rocks, as Roman Leventov pointed out elsewhere), is valuable because, empirically, we observe common structure across those things. What is gained by the FEP is, accordingly, an abstract and general understanding of that structure. (Whether that is useful as a “starting point” depends on how one solves problems, I suppose.)
I don’t understand. Consider the analogous statement: “The laws of physics are applicable to both X and Y, where X and Y are literally any two things in our universe. So the laws of physics are probably a bad starting point for understanding how Y works.”