You want to use "\n" if binmode isn't on.
You want to use "\r\n" if binmode is on.

use List::MoreUtils qw( apply );

for my $bin (0..1) {
for my $eol ("\n", "\r", "\r\n") {
   my $name = $eol;
   $name =~ s/\r/cr/;
   $name =~ s/\n/lf/;
   $name .= '-bin' if $bin;

   {
      open(my $fh, '>', $name);
      binmode($fh) if $bin;
      print $fh map { "$_$eol" } qw( abc def );
   }

   my $file = do {
      open(my $fh, '<', $name);
      binmode($fh);
      local $/;
      <$fh>
   };

   my $data = join ' ',
              apply { s/\x0D/CR/ }
              apply { s/\x0A/LF/ }
              split //,
              $file;

   printf("%-9s %s\n", "$name:", $data);

   unlink($name);
}}
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output

lf:       a b c CR LF d e f CR LF        <- want
cr:       a b c CR d e f CR
crlf:     a b c CR CR LF d e f CR CR LF
lf-bin:   a b c LF d e f LF
cr-bin:   a b c CR d e f CR
crlf-bin: a b c CR LF d e f CR LF        <- want
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Update: Simplified the code a bit.
Update: Oops, removed bug added in simplification. open(my $fh, '>', $file_name) defaults to :crlf, but open(my $fh, '>', \$file) does not!