Isn't it already wide accepted that the Doll was made by Gerhman and he try to breathe a live into it by using the Third Umblical Cord? It's only then instead of bringing it to live, he met Moon Presence, make deal to make the Doll alive in exchange of his own and become the Steward of the dream
There's something that annoys me although it's probably just a bug. The doll in the real workshop keeps moving one of her fingers.
Those "amygdalas" aren't actually Great Ones. According to the guide they are called False Gods. The only Great One Amygdala is the one you fight.
Ah, interesting. Didn't know that. I actually though the lesser ones would be like entities created by the big Amygdala, maybe herself cloning and controlling them all over Yarnham.