When I move books from Intake to Books I get the metadata that is in the format file because I just did a Polish to embed the Intake libraries metadats and then a Modify to reduce it to dc-only and I only copy a couple custom columns when I copy from Intake to Books.
One reason I prefer Sigil for final clean up is because of its idiot-proof metadata edit tool, and I am not saying calibre ought have such a thing - in fact I would argue the opposite.
I have the update metadata option disabled in the calibre editor, I often just use it to looks at a Reports or Live Preview which are 'read only' uses. And there's no point in it injecting non dc metadata, I'll only take them out again
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