For those still interested in the inclusion of nodes into the root of the xml-tree.
With the help of a hint by Hans Hagen, the following is the best I am able to produce.
The code below includes the contents of the file twice as can be seen in the pdf.
\startbuffer[test]
<?xml version="1.0" encoding="UTF-8"?>
<takenotes>
<include file="minimal-example.xml"/>
<include file="minimal-example.xml"/>
</takenotes>
\stopbuffer
\startxmlsetups notes:setups
\xmlinclude{#1}{include}{file}
\xmlsetsetup{#1}{takenotes}{notes:*}
\stopxmlsetups
\xmlregisterdocumentsetup{demo}{notes:setups}
\startxmlsetups notes:takenotes
\xmlshow{\xmldocument}
\stopxmlsetups
\starttext
\xmlprocessbuffer{demo}{test}{}
\stoptext