Prefab Pivot Point

I have a door prefab with a with an empty game object as a parent, which is used to move the pivot point to the side of the door. This is done for door opening/closing animations. But also my doors are instantiated between the midpoint of two walls. So when the doors are instantiated, they aren't created where they're supposed to be, they are half of the door size shifted, because the pivot point is not in the middle of the door. My question is, is there any practical solutions for this, without affecting the animations, how can I solve this issue?