In most cases if you expect XML (or XHTML) as output you better use transformToXML() directly. You gain better control over xsl:output attributes, notably omit-xml-declaration.
Instead of :
$proc = new XSLTProcessor();
$proc->importStylesheet($xsl);
$dom = $proc->transformToDoc($xml);
echo $dom->saveXML();
do use :
$proc = new XSLTProcessor();
$proc->importStylesheet($xsl);
$newXml = $proc->transformToXML($xml);
echo $newXml;
In the first case, <?xml version="1.0" encoding="utf-8"?> is added whatever you set the omit-xml-declaration while transformToXML() take the attribute into account.