How does Polytetrafluoroethylene (Teflon) differ from Polyvinylidene fluoride (PVDF) as a protein binding membrane material?
Essentially you are asking why about the different surface properties of PTFE vs. PVDF.  Generally PTFE is more 'non stick' than PVDF, which is more non-stick than polyethene (PE).  PTFE is much more chemically resistant to corrosion than PVDF or PE.  You are correct to look at the chemical structure.  The more Fluorine atoms on the backbone, the more proteins will not be able to chemically latch onto the surface.  Measuring things like contact angle will confirm this.  I don't know how much the pore structure of the membranes affect things, but from a chemical standpoint, there are clear differences.