When in the Rig configuration inspector, clicking the Apply button will exit the config mode in the inspector and the active scene will stay the rig config one

How we can reproduce it using the example you attached
1. Open the attached project or create a new one
2. Import you're own character model in the project or click on the provided "Dude.fbx"
3. In the inspector, go in the Rig tab and change the rig type to Humanoid and click apply
4. Click on the "Confige..." button to enter rig config mode
5. Modify the mapping on the rig ... easy way is to use the Mapping menu at the bottom and use de Clear and then Automap
6. At that point, the Apply button should be enabled, click on it

Result: The configuration inspector exits and the active remains the "Avatar Configuration" on ... leaving the state of the editor in a limbo state. The only way to exit that is to load an existing scene or create another one. Also, we'll realize that the fbx file hasn't been updated by the apply, even worst, the rig type isn't Humanoid anymore but has been reset to "None" which is a datalost.

Expected: When clicking on the Apply button from the configuration inspector, the inspector should still keep it's inspector and only when we click on "Done" the configuration should exit and flush the "Avatar Configuration" scene to come back to your original scene.

The is a major regression introduced in 2019.1.0a6 and also in 2018.3.0b7
Was working just fine with the previous versions