Import/export config not possible without removing shortcuts

Repeatable: Always, issue is present in GUI and using Drush

Steps to repeat using Drush:
1. Make a new site install at an apache server with Drush 8
2. Change path in settings for config to deploy directory outsite drupal root folder
3. Export a config to the deploy folder
4. Set uuid in deploy module the same as the site uuid
5. Now dev environment is created
6. Clone the site and do a site install for a second environment
7. Enable site deploy module
8. Import config

Both sites need to have the same uuid otherwise config import won't work!

Actual Results:
Import config will fail

If the shortcuts in de second environment are removed the config import will succeed.

You can do the same steps in the GUI, but this has the same issue
Steps to repeat:
1. Export configuration
2. Create second environment
3. Import config