[Xposed Framework Modules] Spere:
I didn't try it for internal sdcard if it matters, but I changed marker from /storage/extSdCard/MyGalaxyNote/Music/ to .scanmusic (should'v been this from the start instead .scanmedia, to get rid of album arts) and it's not seen by scanner. Songs are not appearing to Music Player and what I can see from log is that marker file is not found.

Edit:

Maby you could add option to select "full scan" or this existing scan for marker files. Those not having any problems could keep "full scan" turned off and those having problems (I'm I really the only one?) could force marker file scanning to all directories (even in cost of problems).

Edit 2:

I made tree XMSO/XMSO_sub1/XMSO_sub2/XMSO_sub3/ to both: internal sdcard and external sdcard, every folder including root has all these files: .scanMedia, .scanMusic, .scanPictures, .scanVideo (this time with capital)

All other .scanX files removed, so these are the only ones in my phone.

Then I deleted MediaStore content --> ran Media Scanner and pulled this log:

1133:run
1133:run
1133:run
1133:run
1133:run
XMSO: Intent Intent { act=com.thomashofmann.xposed.mediascanneroptimizer.DELETE_MEDIA_STORE_CONTENTS flg=0x10 } received.
XMSO: Request to delete MediaStore content
XMSO: Modified MediaStore.Files external volume URI is content://media/external/file?deletedata=false
1133:run
1133:run
XMSO: Deleted 1,458 rows from file entries
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Deleted 1458 entries, subText null
XMSO: createSimpleNotification with title Deleted media store content., text null, subText null
1133:run
XMSO: Intent Intent { act=com.thomashofmann.xposed.mediascanneroptimizer.SCAN_EXTERNAL flg=0x10 } received.
XMSO: Request to rescan external volume.
XMSO: onStartCommand is called with Intent Intent { cmp=com.android.providers.media/.MediaScannerService (has extras) }, startId 1, filepath null, mimetype null and volume external on com.android.providers.media.MediaScannerService@42e60fc8
XMSO: startIdsByPid is {28314=1}
Reloaded preferences: {pref_run_media_scanner_as_foreground_service_state=true, pref_prevent_repetetive_scans_state=true, pref_restrict_directories_to_scan_state=true, pref_log_to_xposed_log_state=true, pref_show_results_state=true, pref_logging_enabled_state=true, pref_restrict_to_certain_media_types_state=true, pref_run_media_scanner_with_background_thread_priority_state=true}
XMSO: Number of start commands for external volume is 2
XMSO: Number of successful runs for external volume is 1
XMSO: scan is called for directories [/storage/emulated/0, /storage/extSdCard, /storage/UsbDriveA, /storage/UsbDriveB, /storage/UsbDriveC, /storage/UsbDriveD, /storage/UsbDriveE, /storage/UsbDriveF] on volume external
XMSO: Set service to foreground
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Processing volume external, subText null
XMSO: Searching directories to scan in /storage/emulated/0
XMSO: Marker file exists in directory /storage/emulated/0/XMSO
XMSO: Finished searching directories to scan in /storage/emulated/0. Time: 00:00
XMSO: Searching directories to scan in /storage/extSdCard
XMSO: Marker file exists in directory /storage/extSdCard/XMSO
XMSO: Finished searching directories to scan in /storage/extSdCard. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveA
XMSO: Finished searching directories to scan in /storage/UsbDriveA. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveB
XMSO: Finished searching directories to scan in /storage/UsbDriveB. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveC
XMSO: Finished searching directories to scan in /storage/UsbDriveC. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveD
XMSO: Finished searching directories to scan in /storage/UsbDriveD. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveE
XMSO: Finished searching directories to scan in /storage/UsbDriveE. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveF
XMSO: Finished searching directories to scan in /storage/UsbDriveF. Time: 00:00
XMSO: The following directories will be scanned by MediaScanner: [/storage/emulated/0/XMSO, /storage/extSdCard/XMSO]
XMSO: Changing thread priority in MediaScanner constructor
XMSO: In android.media.MediaScanner#processDirectory prescan
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/emulated/0/XMSO, subText null
XMSO: The file /storage/emulated/0/XMSO/.scanMedia should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/.scanMusic should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/.scanPictures should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/.scanVideo should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/.scanMedia should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/.scanMusic should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/.scanPictures should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/.scanVideo should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/.scanMedia should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/.scanMusic should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/.scanPictures should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/.scanVideo should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanMedia should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanMusic should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanPictures should not be considered as a media file
XMSO: The file /storage/emulated/0/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanVideo should not be considered as a media file
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/extSdCard/XMSO, subText null
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanMedia should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanMusic should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanVideo should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/XMDSO_sub3/.scanPictures should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/.scanMedia should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/.scanMusic should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/.scanVideo should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/XMSO_sub2/.scanPictures should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/.scanMedia should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/.scanMusic should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/.scanVideo should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/XMSO_sub1/.scanPictures should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/.scanMedia should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/.scanMusic should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/.scanVideo should not be considered as a media file
XMSO: The file /storage/extSdCard/XMSO/.scanPictures should not be considered as a media file
XMSO: In android.media.MediaScanner#processDirectory prescan
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Postscan, subText null
XMSO: scan(String[] directories, String volumeName) has finished scanning external
XMSO: createBigTextStyleNotification with title Media Scanner Optimizer, text Scan directories time 00:00, subText Volume external (Expand for details), inboxSummary Volume external
XMSO: stopSelf is called on MediaScannerService
XMSO: Received intent Intent { act=pref-xmso flg=0x10 }
XMSO: Reloading settings due to broadcast.
Reloaded preferences: {pref_run_media_scanner_as_foreground_service_state=true, pref_prevent_repetetive_scans_state=true, pref_restrict_directories_to_scan_state=true, pref_log_to_xposed_log_state=true, pref_show_results_state=true, pref_logging_enabled_state=true, pref_restrict_to_certain_media_types_state=true, pref_run_media_scanner_with_background_thread_priority_state=true}