IMO, one possible solution to this problem could be to allow the user to specify two different source groups.
Currently, you can specify as many folders as you wish, but they are all included in the same group, and all files are checked against each other. With two different source groups of folders, you could consider that group 1 must NEVER be touched, and group 2 contains potential dupes of files in group 1. So, it would be easy to list the files in group 1 as the headers (with no similarity percentages), and beneath them, the files of group 2 only.
File 1 of group 1
- File N1 of group 2 - 100%
- File N2 of group 2 - 80%
File 2 of group 1
- File N3 of group 2 - 90%
etc...
Since File N1 of group 2 is in group 2, it will not be listed as a header file, and similarly, the files of group 1 will never be listed as potential dupes.
(That method is supported by Audio Comparer, and I like it. But AC is not a good product, it is extremely slow, it misses most similar files, and it is not free.)
Of course, it is still necessary to support the current method, to find similarities within a single group. In that case, perhaps a good improvement would be to highlight the files that have already been listed above in the list in a different color.