One possibility to avoid having say xenc-schema.xsd included is to re-do that by hand from scratch as JAXB beans. (but not just copying what JAXB makes for us under target/generated-sources!)
Not sure how 'clean room' this has to be.. I know many of these standards 'by heart' so I guess it can't be me? Perhaps I will need to write out a requirement document?
We can also cheat to our heart's delight here as we don't use all the features of the schemas - we just want documents using those elements to not fail parsing.