Steps:
1. Create a new project
2. Add Cube to the Hierarchy
3. Make a prefab out of this cube
4. Make a variant out of this cube
5. Make a variant of the variant of the cube
6. Open Variant of Variant and remove BoxCollider component
7. ApplyAll to Base
==>
Removed BoxCollider is shown as override in the first level Variant
8. Remove MeshRenderer from the Variant of Variant
9. ApplyAll to Base again
==>
MeshRenderer component is removed from Variant of Variant but BoxCollider reappears

Expected: No BoxCollider in Variant of Variant asset

Please, take a look into attached movie for details