Here is a simple example:
1. Create an Empty GameObject called "Root"
2. Create an Empty GameObject as a child of Root, called "Test1"
3. On Root, create an FSM with one state
4. Add action Debug GameObject, on GameObject field create a variable called TestObject1.
6. Assign TestObject1 to Test1
7. Turn Root into a prefab
8. See that in both the Scene, and the Project Window that TestObject1 is set to Test1.
All is well, a prefab is referencing another gameobject which happens to be it's child.
Then:
9. Turn the Root FSM into a Template.
10. See errors on the Debug GameObject action about referencing scene objects.