I assume that you cannot use the Find Duplicates plugin to do what you want, so I infer that you want to find books in a cross-library intra-book search. So, yes, you could, but only by specifying the search criteria that would match books in the current library if you were to execute that identical search from the other library. MCS has no specific "find duplicates" functionality, however, since there was already a Find Duplicates plugin when it was created.
DaltonST
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