If albums/files have already been loaded, and the config option "Save cover images as separate files" is changed before the files are saved, that config change is ignored, and the setting for this option when the files were loaded is used.  I'm guessing this same problem may affect other Cover Art settings too.

I often find that I've already loaded files before I realize I want to change Option Profiles that affect Cover Art settings, but am annoyed when my settings changes are ignored when saving those files.