If you (accidentally) selected a project to apply your customizations to, a confirmation message similar to the one below will appear.

This can be confusing, possibly making you think the customizations have been applied to the project after all. This is not the case, and the customizations have not been applied to the model package either. You should only apply your customizations to a tracked or shared model package, not to a project.
- Perform the Apply command again, and select the tracked or shared model package you want to apply the customizations to.