My code is below - it's not drastically different from yours one. You're right - recursion is unavoidable. I hoped to avoid that with some XML::LibXML options - no way...

my @list = ();
my $parser = XML::LibXML->new();

sub Process($)
{
  my $f = shift;
  if (-f $f and -r $f)
  {
    if (scalar(grep($_ eq $f, @list)) == 0)
    {
      push @list, $f;
      my $root = $parser->parse_file($f)->documentElement();
      my $prefix = $root->lookupNamespacePrefix('http://www.w3.org/200
+1/XInclude');
      if ($prefix)
      {
        my $ok = 1;
    foreach my $xincludeNode ($root->getElementsByTagName("$prefix:inc
+lude"))
    {
      my $xincludeFilename = File::Spec->rel2abs($xincludeNode->getAtt
+ribute('href'));
      $ok &&= Process($xincludeFilename);
    }
        return $ok;
      }
      else
      {
        return 1;
      }
    }
    else
    {
      return 1;
    }
  }
  else
  {
    print STDERR "The file '$f' isn't found or not readable\n";
    return 0;
  }
}
  
Process(File::Spec->rel2abs($ARGV[0]));
my $list = join("\n", @list);
print $list, "\n";
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