From what I’ve read you can do this by calling the below method on Document before creating the DOMSource:
doc.setXmlStandalone(true); //before creating the DOMSource
If you set it false you cannot control it to appear or not. So setXmlStandalone(true) on Document. In transformer if you want an output use OutputKeys with whatever “yes” or “no” you need. If you setXmlStandalone(false) on Document your output will be always standalone="no" no matter what you set (if you set) in Transformer.
Read the thread in this forum