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In my previous comment's screenshot of the "Adding actions" dialog window, there is a checkmark in the box for "Auto-merge added books if they already exist". But that was just for the screenshot.
I actually currently have my Calibre to not auto-merge added books. When I do add books which Calibre thinks are duplicates, Calibre provides a prompt and asks me if I want to add the newly added (but duplicate) books or not. I noted it doesn't ask me if I want to merge or how to merge.
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