It seems to denormalize the output and include the namespace context along with the nodes that really need the namespace context.
For example, the web page for this question contains the built-in creativeCommons namespace:
<feed xmlns="http://www.w3.org/2005/Atom" xmlns:creativeCommons="http://backend.userland.com/creativeCommonsRssModule" xmlns:thr="http://purl.org/syndication/thread/1.0">
<creativeCommons:license>http://www.creativecommons.org/licenses/by-nc/2.5/rdf</creativeCommons:license>
</feed>
When you output xml using this script:
def root = new XmlParser().parseText("http://stackoverflow.com/feeds/question/227447".toURL().text)
println new XmlNodePrinter().print(root)
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<feed xmlns="http://www.w3.org/2005/Atom">
<creativeCommons:license xmlns:creativeCommons="http://backend.userland.com/creativeCommonsRssModule">
http://www.creativecommons.org/licenses/by-nc/2.5/rdf
</creativeCommons:license>
</feed>
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