I currently use Module::Build with a traditional Makefile.PL generated

I don't think you're going to be able to get this to work while automatically generating a traditional Makefile.PL with Module::Build. You'll need both your Build.PL and Makefile.PL to have the OS-specific dependencies.

Another possibility is try Module::Install and you put the OS-specific dependency logic there and let it generate your Build.PL and/or Makefile.PL... but that is just another wrapper around the problem. For example, from the Pod, an example from File::HomeDir:

  use inc::Module::Install;
  
  name           'File-HomeDir';
  all_from       'lib/File/HomeDir.pm';
  requires       'File::Spec' => '0.80';
  build_requires 'Test::More' => '0.47';
  
  if ( $MacPerl::Version ) {
      # Needed on legacy Mac OS 9
      requires 'Mac::Files' => 0;
  }
  
  if ( $^O eq 'MXWin32' ) {
      # Needed on Windows platforms
      requires 'Win32::TieRegistry' => 0;
  }
  
  auto_install;
  WriteAll;
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