My tools do something similar. OnDirCreated can block a dupe dir creation and DupeLister can add dirs to the dupelists.
THere are issues you need to know tho:
1-adding dirs that are incomplete is silly
2-any dupe finder needs to be FAST (like mine) that means you shouldnt add entries by hand (unless you sort the file again).
I dont know if it combines well with iobanana tho, so that is up to you to try out.
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