There’s no way to tell DEVONthink, that these are no duplicates and that’s ok, because should come a real duplicate of these files around, they will be a duplicate, so you might want to recognize them.
I have many of such false duplicates too and my database gets constantly filled with real duplicates, so I check for duplicates from time to time with a smart group (Instance is Duplicate).
I have assigned a label to those false duplicates, so that I don’t have to check them again and again when I sort out duplicates, but I only label those false duplicates as false duplicates that are so unique, that chances are almost zero, that they will see a real duplicate ever. Still I don’t exclude them from the smart group (which would be otherwise: Instance is Duplicate + Label is not ‘false duplicate’), so that duplicates of them don’t slip through.
DEVONthink needs an improved recognition of duplicates.