ckeditor.config.js is not loaded from the correct location (when Devel module code block enabled)

I'm having an issue where CKEditor module is not respecting the specified load locations given in the configuration settings (in Drupal, not the config file).

Basically, if I add ckeditor.config.js to my theme, it gets loaded correctly, but the the original config file from the module gets loaded after it, either overwriting my settings, or adding to them.

The same issue is occurring with ckeditor.styles.js, however it is just overwriting my styles altogether.

Deleting the original ckeditor.config.js seems to fix this.

An additional side effect, is that if the theme has a theme parent, and the theme parent ALSO has a config file, that file is loaded as well.

It seems that CKEditor should either:
a) Only load the specified config file
- or -
b) Load the module => parent => theme, so that they are overridden in a useful order