What happened?

Description

We noticed that when we added the media embed button to CKEditor, that project config change was accidentally being reverted by other developers because craft up was not applying the CKEditor config change.

Steps to reproduce

1. Take a database snapshot.
2. Add a button to the CKEditor config and commit project config changes.
3. Revert to your database snapshot that does not include the project config change for CKEditor.
4. Run craft up (see screenshot for my result; you can see it didn't pick up the config change)
   
5. Run craft project-config/apply (see screenshot for my result; you can see this did pick up the config change)
   

Expected behavior

I expect craft up to pick up all config changes per the description of the CLI command.

Actual behavior

craft up is not picking up our CKEditor change. Not sure if this could be a downstream issue with the plugin or something with Craft more globally.

Craft CMS version

4.9.7

PHP version

8.2.20

Operating system and version

Linux 6.9.6-orbstack-00147-gb0567c7c0069

Database type and version

MySQL 8.0.36

Image driver and version

Imagick 3.7.0 (ImageMagick 6.9.11-60)

Installed plugins and versions

CKEditor: 3.8.3