Something causes to add new default value to some config files without deleting the old ones

This happened while I was trying to perform following failed updates using drush commands and checking in the UI their corresponding checklist items.

varbase_core_optional_update_8701
varbase_core_optional_update_8702
varbase_core_update_8703

Background: I tried to update directly from 8.7.0 to 8.7.2 using ./bin/update-varbase.sh which occured to me that it went pretty flawless. But after I saw that the updates above were not done.

Now when I go and hit Save in the Update Helper checklist, this happens again again. In the following config files, the default values are added each time. One of them looks like this for now:

uuid: 0f4abf4e-dc55-48e4-b277-75a8a82d13cf
langcode: en
status: true
dependencies:
  config:
    - field.storage.media.field_media_in_library
    - media.type.audio
_core:
  default_config_hash: uYbxxRye1RV8Cn73W5FtIKyn4d3TJEYFi7MoFYMi_bQ
id: media.audio.field_media_in_library
field_name: field_media_in_library
entity_type: media
bundle: audio
label: 'Show in media library'
description: ''
required: false
translatable: true
default_value:
  -
    value: 0
  -
    value: 1
  -
    value: 1
  -
    value: 1
  -
    value: 1
  -
    value: 1
default_value_callback: ''
settings:
  on_label: 'On'
  off_label: 'Off'
field_type: boolean

The config export is like following after hitting Save in Update Helper. The affected files are only the ones starting with field.field....

$ drush cex sync
 [notice] Differences of the active config to the export directory:
+------------+-------------------------------------------------------+-----------+
| Collection | Config                                                | Operation |
+------------+-------------------------------------------------------+-----------+
|            | field.field.media.audio.field_media_in_library        | Update    |
|            | field.field.media.file.field_media_in_library         | Update    |
|            | field.field.media.image.field_media_in_library        | Update    |
|            | field.field.media.remote_video.field_media_in_library | Update    |
|            | field.field.media.video.field_media_in_library        | Update    |
|            | embed.button.gallery                                  | Update    |
|            | embed.button.media                                    | Update    |
|            | checklistapi.progress.update_helper_checklist         | Update    |
+------------+-------------------------------------------------------+-----------+

I am going to correct them manually and drush cim to prevent any future errors.

In Update Helper all items of 8.7.1 are checked but warnings report that they are failed to be done automatically. (But this may not be directly related to this issue)

This update failed to be done automatically.
Try running drush varbase-up --force varbase_core varbase_core_optional_update_8701 to force applying this update. This will likely override your previous configuration! Do this on your own risk.