Find duplicates PI really has 2 modes.
You want to use the alternate:
Find Library Duplicates.
Note: This mode has its perspective from WHICH LIBRARY it was launched from (Calibre is viewing).
So if you launch from the SOURCE, looking at (the path was entered) the Target, it will show those that have ENTRIES in the target.
I point this out, because those might be 'empty books'. Read the details of the found dups

they will tell what formats if any