As agreed with theducks I have moved the related posts above into this plugin thread from the Plugin Ideas one as I intend to support it in this plugin.
To directly respond to your latest post - indeed your workflow is very slightly different but I think effectively it is the same issue - Save to disk writes three files, remove from disk only removes one of them
I had implemented a function in Quality Check which just pruned the (effectively empty) folders. I will extend that to also remove any orphaned .opf files. It already handles that if you only had one book per folder, but of course as per your template you can have multiple books in a folder and will just want the .opf files removed.
I am curious though - you don't have a cover in there too. Is that because you have that particular save to disk option turned off?