Using 'One file per directory' to get one file per directory works fine provided the output lines are in directory order... but if they are not, each directory's file contains the output of only the last group of files in that directory. It seems upon each directory change mp3tag is opening that output file as empty, erasing any existing content, whereas each time except the first it should be opening for appending.
A workaround is to surround the export config file content with
I've though about this again and I think I see your point now. What you expect is that the Export creates one file of per directory regardless how the file list is sorted. I'll look into this again, but it won't append the results to an existing file (unless you enable the append option).