read and readline (<>) are buffered, so it's not that bad. If you need Perl-side buffering, the following would be much better:

use constant BLK_SIZE => 64*1024;

{
   open(my $FILE, "file.binary") or die $!;
   binmode($FILE);

   while (read($FILE, my $buf, BLK_SIZE)) {
      for my $byte (unpack('a*', $buf)) {
         ...
      }
   }

   close $FILE;
}
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