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If I understand correctly -- you want to be able to use a pre-existing standalone feature (select which book is the master copy during Merge) in the Add books ==> Auto-merge feature?
Personally, I would stay away from auto-merge, and handle it all manually.
I believe the automerge is intended only on the theory that you have a lovingly fine-tuned library, but got new formats. And the metadata inside a book is likely to be inferior to the cleaned-up metadata in your library.
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