The difference between your observed and expected output appears to be down to canonicalisation. See eg:

#!/usr/bin/env perl 
use strict;
use warnings;
use XML::LibXML;


my $dom = XML::LibXML->load_xml (string => <<'EOT');
<?xml version="1.0"?>
<header>
   <id x_id="1">
      <a/>
      <b/>
      <c>as</c>
   </id>
</header>
EOT

print "\nNot canonical:\n\n" . $dom->toString;
print "\nWith canonical:\n\n" . $dom->toStringC14N;
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