Indeed, so given that the search system cannot meet his needs, he really only has two options I can see:
(1) Extend the Find Duplicates plugin to filter the results
(2) Give up on the idea of trying to filter the results, and instead write a plugin that does more intelligent merging.
And I totally agree that merging formats just because they are of different types regardless of their source is a recipe for a library mess. Still, some users really don't care that much. It isn't the way I personally manage my library which is why I am only lukewarm to the idea, but there are people out there who don't share my philosophy on content quality. Which is completely fair enough given how time consuming it can be.