Hi,
If you don't use Odfconverter to do the transformation:
$docx->transformDocx('pages-word2-output-1-This-is-my-amazing-title.docx', 'example_text.pdf', null, array('odfconverter' => false));
The PDF will include the line numbering. We're going to check OdfConverter to find any issue but this is a quick solution if your documents don't use complex tables.
Regards.