public class MyResourceFactoryImpl extends ResourceFactoryImpl {

    // ...

    @Override
    public Resource createResource(URI uri) {
        XMLResource result = (XMLResource) createResourceGen(uri);

        result.getDefaultSaveOptions()
                .put(XMLResource.OPTION_KEEP_DEFAULT_CONTENT, Boolean.TRUE);
        result.getDefaultLoadOptions()
                .put(XMLResource.OPTION_RECORD_UNKNOWN_FEATURE, Boolean.TRUE);
        // ...

        return result;
    }

    // ...

}