@Jarl
Not sure if this is what you meant when you said "The constructor example clearly shows that version and encoding only end up in the XML header", but you can also affect other parameters in the generated XML header, by accessing the DOMDocument's properties, for example:
<?php
$dom = new DOMDocument('1.0', 'UTF-8');
$dom->xmlStandalone = false;
echo $dom->saveXML();
// <?xml version="1.0" encoding="UTF-8" standalone="no"?>