The summarization comes from the content of the current document. The annotation file is a separate document associated with the referring document.
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You can make your annotations in the PDF and use the Summarize Annotations command to create this separate document.
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Also an alternative, you can create an annotation file – which is what you were doing in the screencast – and make notes in the internal document.
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And yes, you could use both annotating in the PDF and taking notes in an annotation file.