The library you linked can be used only for converting JATS XML to other formats like HTML. Or at least that is how I have been using it.
I used it in the embedGalley plugin that converts JATS XML galleys on the fly to HTML and shows them on the article abstract page (https://github.com/ajnyga/embedGalley). Unfortunately I have not had the time recently to take the plugin further, but I do have plans to do that in the future.
For converting articles from docx to JATS XML I have used the OTS-service. But as you noticed, there are still problems there.
I have been scetching a workflow that any journal editor even with limited technical skillset could use to create JATS XML articles and PDF’s. You can find the scetch here: https://github.com/ajnyga/OJS3XMLWorkflow. It is work in progress - at the moment I think that we are missing the needed tools, but I think that we will get there soon. I am hoping to have time for this next summer…
If you have technical skills to use for example command line tools, then I suggest that you look into @Vitaliy’s work. I think that he has a command line conversion script for docx and a more sophisticated plugin for visualizing JATS XML. I do not know the details, but maybe he can add a link here.