Deduplication tool which is able to only compare two directories against each other?

I tried rdfind and jdupes, and if I specify two directories for them, they both match not only files in one directory against other directory, but also files inside of one of the given directories against each other. I would like to exclude such results which reside in one directory only, and it would also be faster to avoid scanning them. But I couldn't find an option in neither of tools which allows that.