What are best practices to solve `All files/directories will have '-rwxr-xr-x' permissions` when building docker images on Windows?
It is not currently possible to disable that warning, see discussions on Issue 20397:


  That warning was added, because the Windows filesystem does not have
  an option to mark a file as 'executable'. Building a linux image from
  a Windows machine would therefore break the image if a file has to be
  marked executable.
  
  For that reason, files are marked executable by default when building
  from a windows client; the warning is there so that you are notified
  of that, and (if needed), modify the Dockerfile to change/remove the
  executable bit afterwards.


In a sense this also means it's practically impossible to actually solve the issue.

What maybe can help a bit is moving the error message from stderr to stdout, released in docker 17.04. See Issue 29856.