Currently the only thing I can get Find Duplicates to do is compare all images to all other images within a directory (or set of multiple selected directories), or to compare a single image to a set of albums/directories.

Based on the Restriction options to Include/Exclude the "Reference Album[s]" I at first thought there was a way to select a reference set and find all duplicates of that reference set within a target set.

Specifically, I imported a folder of images and wanted to see if any of them were duplicates after importing as I had not yet set up the fingerprints. I didn't want to search every image in my collection against every other, just every image I had just import against the rest of the collection--still a long task but much shorter! 

After a lot of troubleshooting there didn't seem to be a way to do this. If there was a way to do it, there was at the very least no clear way to tell what the "Reference Album" was currently set to other than the (usually empty) window of "Reference Images" containing already suspected duplicates. This is, for me at least, a really important feature for making Find Duplicates and other Similarity Searches more useable--searching either one image at a time or checking an entire set against itself are both very wasteful tasks compared to what I find myself actually wanting to do with the feature!