Currently, the position, rotation, and scale of sub-objects in a prefab is stored for each scene. If you have a prefab that contains a door frame and door, for example, you can place the prefab and then make the door opened or closed, and that new orientation of the door piece will be stored in the scene. If you edit the original prefab file, other properties will update when the scene is reloading, but changing the position of the door piece in the prefab file will not affect the subobject in scenes where it has already been placed.
The other way of doing this would be to always get prefab orientations from the prefab file. This means if you have a prefab that is an assembly of parts, you would not be able to adjust the position or rotation of any sub-object in the editor, because it would be locked in place, relative to the parent. The only way to make the door opened, for example, would be to unlink the prefab, after which it will not refer back to the original prefab file, and will not get updated if anything in the prefab is changed.
Which do you think is a better design choice for the majority of the time?