If you look in the docs for XML::LibXML::Node you will see:

isEqual
deprecated version of isSameNode().

isSameNode
returns TRUE (1) if the given nodes refer to the same node structure, 
+otherwise FALSE (0) is returned.
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In other words, it checks to see if it is the very same node, so even if you change the prefix of the second element (in $xmls2) to Z1, isEqual() will still return false. I assume isEqual() has been deprecated because of this.

You could have a look at localname() in the XML::LibXML::Node docs, and setNamespaceDeclURI() and setNamespaceDeclPrefix() in the XML::LibXML::Element docs.