What if you generate classes from the xsd's you downloaded, but instruct it to use org.docx4j.wml and org.docx4j.dml package names? see inside the wml xsd for how to do this ... jaxb:package annotation.
Then replace org.docx4j.wml.* with the classes you generated.
You will still have an issue, which is that my version of the wml schema modifies some of the generated class names eg so we have PPr.java, not CT_PPr.java.
So either you will need to change any references in docx4j to use your class names, or stick with the docx4j names, and modify any references in your pptx, xslx packages. If there is just a few, this could be easy.
Or, as you say, you could use the xsd included in docx4j. This might be easier. I've never seen the error you mention (but I generate the wml and dml classes using separate runs of xjc .. running xjc on wml.xsd generates a subset of the dml stuff (ie the subset that wml.xsd imports) - see comments in dml-stylesheet.xsd .. its a little messy. In the comments at the top of wml.xsd, you can see which version of xjc I use to do the build.
ERROR] XJC while parsing schema(s) file:/D:/workspace/word-beans/src/main/resources/dml-picture.xsd[74,35]: org.xml.sax.SAXParseException: src-resolve: Cannot resolve the name 'a:CT_NonVisualDrawingProps' to a(n) 'type definition' component.
This looks like an xsd:include|import pointing at an incorrect file path. If you can ensure your downloaded pptx, vml, and xslx point at the existing docx4j schemas everything should just work.
What version of JAXB are you using, and where did you download the schemas from?