The motivations of the Amygdalae are unknown. It's clear that the godlike beings could likely send Yharnam toppling to the ground if they wished. The weapons of mortals pale in comparison to the Great Ones. It's odd really, how they seem so idle and passive as they watch the humans walk by, sometimes reaching down in curiosity to grasp at one. Amygdalae only appear in places of worship. One is found wrapped around the Oedon Chapel, another in the abandoned Church that served as a gateway to Yahar'gul. The Amygdala the player fights is located in what appears to be a large cathedral, where the ancient Pthumerians likely worshiped the Great Ones. Consider the Moon rune's description:

"A transcription of "moon," as spoken by the Great Ones inhabiting the nightmare. The Great Ones that inhabit the nightmare are sympathetic in spirit, and often answer when called upon."

Perhaps that explains why the Amygdalae which live in the Nightmare congregate around places of worship. Maybe they listen to the hopes and prayers of human beings. In Yahar'gul however, the Amygdalae are everywhere.
“Grant Us Eyes”~