I ended up with some time to spare today at work and was able to play around with this. Apparently the answer to my question is Calibre ignores *all* incoming metadata in favor of what's already associated with the record. Even when there wasn't a book originally attached and the incoming copy has one. This is using the Overwrite Existing Duplicate Formats.
To me, that isn't overwriting and defeats the purpose for telling Calibre to overwrite existing duplicates. And if that's the default behaviour of Overwrite I'm not sure why it's even an option.
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