By definition, enveloped transform returns the node set that contains all the nodes in the document except the <dsig:Signature> subtree. If you want to sign only a content of a particular node then you probably need to use XPath transform instead. If you can achieve your goal with template and xmlsec utility then imgrating to a dynamically created templates is pretty straigthforward: just call correct functions in correct order (and you always can dump the dynamically created template to a file to verify that you are creating exactly what you want).
And there is no difference between missing and empty URI attribute in the <dsig:Reference> element.
Aleksey
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