True.
But, honestly, MP3tag is a program to tag files and not a file renaming program. You don't even see which other files are also in the scanned file system. So how should MP3tag guess that a certain other file is the cover belonging to an album.
This connection is only establshed if the picture data has been embedded.
Also true if you do not delete them with means of the OS.
After you have imported the picture files you could
open a command shell
navigate to the top folder
enter the command del /s cover.jpg
and all files with the name cover.jpg in all the subfolders will be deleted.
The you could export the picture data and probably only the new images will be there.
iIn addition to what ohrenkino wrote:
Files other than music files are normally not displayed in Mp3Tag. You can change this if you want by adding the file extensions used for cover files to Mp3Tag under File->Options->Tags->Restrict incoming files to. Then the cover files will also be displayed in the list view of Mp3Tag.
However, these cover files do not have any metadata that Mp3Tag can use. So the only option is to use placeholders that are not metadata assigned to the file.
This includes, for example, %_directory% and %_parent_directory%.
So if you have set up your file structure according to the scheme Albumartist\Album\Files, for example, you could mark the cover files and rename them with the format string %albumartist% - %album% in the converter Tag->Filename or a corresponding action of the type Format Value for the field %_filename%.