As far as I know Tamino doesn’t modify the document with and ino:id or ino:docname etc.
These are introduced when a query result is returned.
The query result contains a node list and the ino:id etc is a label to tell you where the nodes come from.
The clue is that queries don’t return documents they return nodes from within the document set in the collection you are addressing.
The document you get back with a query is a represntation of a node set as a parseable XML document.
The REAL document comes back with the GET by reference which is either an ino:id reference or a doc:name reference.
If you link about in these terms it may begin to make sense. 
#webMethods#API-Management#Tamino