Do you know of a JAXB setting to prevent standalone="yes" from being generated in the resulting XML?
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
This property:
marshaller.setProperty("com.sun.xml.bind.xmlDeclaration", false);
...can be used to have no:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
However, I wouldn't consider this best practice.