So unless I'm misunderstanding something, this is the way everything works:
The shadows are originally small non-sapient soot creatures, not unlike the clingers. These mimics/morphs are probably normally harmless.
Through Grandfather's multi-phase process, the mimics are made to mimic a human (or living doll), form a sense of self, develop the ability to control soot, and finally take over the human they mimic, becoming a complete being, but with soot powers. We see an example of a living doll being taken over by a clinger, where it gets inside them and takes control. Presumably the result of that isn't the same as it would be for a proper shadow.
Things that aren't clear:
What is Grandfather's purpose for all of this? Sure, making superhumans, but to what end? Are they actually nobles in some kingdom? Do they rule the world? Are they planning to?
What is Grandfather? Is he simply the first of his kind, created by chance? Or is he not a proper shadow-sama at all, but simply a soot ghost that hung around long enough to become intelligent?
Speaking of ghosts, what are they? And clingers, too. Originally they were said to be the bad emotions of the shadows given form, but that was when we didn't know much about anything. I doubt these are a natural occurrence that would happen when the mimics are in their natural habitat, wherever that is. Maybe they are morphlings, offspring of shadows.