Publishing with APS open access with a CC-BY license on a preprint server
I got a reply from APS on this issue. My question was: 


  We accidentally chose the CC-BY 4.0 license https://creativecommons.org/licenses/by/4.0/ for our arXiv preprint of a manuscript submitted for publication in Physical Review Letters instead of the standard arXiv license.
  
  Does this license conflict with the standard Transfer of Copyright
  agreement? If so, is it possible to instead choose the option "Retain
  copyright and complete the Creative Commons publication agreement"?
  
  As far as I understand, the second option should work, since APS would
  publish under the same CC-BY 4.0 license as we used for the arXiv
  submission. Is this correct?


APS answered:


  Choosing a CC-BY-4.0 license for your arXiv submission does
  not conflict with choosing the standard Transfer of Copyright
  Agreement for submission to an APS Journal.


So in short, you can use a CC-BY-4.0 license for your arXiv preprint and still publish the manuscript in PRL under the usual conditions (i.e., not open-access).