The XML I am expecting is supposed to be only one url/urn (xmlns:urn=\"urn:123:456\") like below:
You could declare both namespaces, e.g.
<xsl:stylesheet version="1.0"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:ns1="urn:123:456"
xmlns:ns2="urn:789:123"
exclude-result-prefixes="ns1 ns2">
Then use a union expression for your matches and selections, for example:
<xsl:template match="/ns1:Document | /ns2:Document">