Also my DOCX2JATS converter in not ideal. I am planning fully upgrade it next year. It works good only if one apply very strict standards inside docx. Put citation in Vacouver style, explicitly point titles of sections etc. If you want to use it, pay attention at examples of our docx files.
But JATS Parser Plugin is good enough for production use. So, if you would manage to create valid JATS XML, it will be displayed appropriately.