Using Make Unique prevents changes to the top-level material instance from affecting the sub-material instance within the Multi/Sub-Object material.
You can also use Make Unique at the map level, when a map is instanced to different components of the same material.
Example: Create an instanced sub-material:
At this point, the material applied to the sphere and the sub-material are instances of each other.
Make Unique is not available for the top-level instance of the sub-material.