[Xposed Framework Modules] Portgas D. Ace:
When going through all the stuff in the OP, one can find this:

The Xposed Media Scanner Optimizer settings application can be started from the launcher and allows you to configure the following settings:

Repetitive Scans: If this preference is checked repetitive scans at boot time will be prevented. Repetitive scans are not necessary and only cause greater battery drain. Depending on the Android version and vendor repetitive scans may occur and can be prevented by checking this preference.

Service Importance: When checked the media scanner will run as foreground service and its operation will be visible to the user via a notification.

Thread Priority: If checked the media scanner will be forced to run with background thread priority even if it is running as a foreground service. This is the suggested setting. If unchecked the thread priority depends on whether it runs as a foreground service or not.

Directories: If checked the media scanner will only scan directories that have a .scanMedia file (i.e. an empty file with a dot as first part of the name similar to the .noMedia file). Use a file explorer app to create this file. This file can be placed in a directory that may contain subdirectories. The subdirectories will be scanned as well. If unchecked all directories will be scanned (except for the ones containing a .noMedia file - this default behavior of the media scanner is not altered by the Xposed Media Scanner Optimizer).

Media Types: If checked only certain file types will be scanned. To define which file types the scanner will scan in a directory create the following files: .scanMusic, .scanVideo and .scanPictures. So for a directory containing a collection of music albums you would need to create a .scanMusic file at the directory that contains all albums if you only want the music files scanned. Images contained in the album directories would then be skipped.

Run automatically: If checked the media scanner will scan whenever it is told to do so by the system. If unchecked it only scans the external volume when triggered from the XMSO app. Requests for the scanning of single files still work in either case.

Result Notifications: If checked a notification will be shown when the scanner has finished including information about the scan time.

Trigger Media Scanner: When touched a media scanner is triggered.

Delete Media Store Contents: When touched the contents of the media store are deleted. This will not delete the actual files on the storage. Trigger a scan or reboot to let the scanner populate the media store after deleting its contents. This is useful if the media stores already contains entries that you do not want like images from all directories in the Gallery. First check the preferences to restrict what will be scanned, empty the media store and trigger a rescan. After the rescan only what has been scanned depending on your preferences will appear in the Gallery.

Android Logging: If this preference is checked details of the media scanner and the Xposed module are written to the Android log. This is useful for development and to troubleshoot. For end users this should stay unchecked.

Xposed Log: If this preference is checked details will be written to the Xposed log. Since the Xposed log is persisted this is also useful for troubleshooting. For end users this should stay unchecked.

Was desperately searching for a solution in the first place, too. Now everything works fine for me. Concerning top folders: haven't dealt with this excessively, so I can not help you with this issue beside the things I have already written.

[MENTION=3542212]thomashofmann[/MENTION]: suggestion: show some kind of tutorial when the user starts your module for the first time, so there is less confusion :)