Hello,
Comments are not supported in the native conversion plugin (https://www.phpdocx.com/documentation/conversion-plugin/preparing-the-templates-for-its-conversion Supported OOXML tags and attributes when using the native method section), we recommend you using the libreoffice conversion plugin. In the docs folder included in the package you can find how to include the comments to the PDF margins if needed.
phpdocx 12 supports adding comments, footnotes and endnotes at the end of the document using the native conversion plugin.
Regards.