By default SongKong doesn’t rename files only fix the metadata within the files, but this is easy to change by modifying the value of Rename files based on metadata from No. We recommend setting to Yes if matched to a release so that files are only renamed if SongKong has good data for them otherwise bad metadata could be used to rename.
The actual rename mask is set on the Filenaming tab, you can specify one for usual albums and a different one for Various Artists albums, there are many to choose from
and you can also create new masks or modify them in Preferences.
I am pretty sure I just now ran your shown settings on the three folders. Here is what I have now. And, at this point, the third folders appear to just be folders without files. So, is there a way to further clean these up?
No, SongKong should delete empty folders but it doesn’t always, there is a bug somewhere that has already been reported.