Apply Prefab Instance does not register unused overrides

Steps:

1. Open attached project
2. Load SampleScene
3. Select child GameObject (Nestee) and tick "Is Trigger" on the BoxCollider
4. Delete Nestee prefab instance 
5. Select Nestor prefab instance 
6. Open Override window and ApplyAll

Expected: Nestor prefab instance has unused override (m_IsTrigger)

Actual: No Overrides is show for Nestor prefab instance