In the Find panel with Indexed search set to Global Everything, the fields Find in and Exclude work properly. Find in is greyed out, and the items in Exclude are skipped.
The Duplicates Finder with Indexed search gets it wrong: the Find in field is not greyed out, and the items in Exclude are not skipped.
The Global Everything index returns both files and folders. This is wanted for the standard Find functionality, but the DupeFinder should exclude folders automatically when set to MD5 Checksum comparison. On the C: drive alone are over 90.000 folders that could prevent the DupeFinder from doing its job.
(edit: clarify comparison mode)
Another idea: How about showing the index size (number of files and folders) that results from the settings in the Exclude and the Indexed search fields? This will be particularly useful if the index exceeds Preferences / Miscellaneous / Advanced: [Limits] everything_max_results.