exposed properties ignore prefab apply

I have had a bit of a dig around and it doesn't look like you can, does anyone know of a work around for telling an exposed properties on a script to not change when applying a prefab. For example: I have a script which changes a UI element's RectTransform based on ScreenOrientation, and I have about 20 instances of a Image Prefab, on each script has different exposed values which I want to keep, but if i wanted to update for example the colour of the image, I can do it to one and it will change the other instances but it will also change the exposed values in the sript, which ruins the entire scene.

I have been putting this problem in the too hard basket for too long, i need to figure this out, because it seems like a feature that should be pretty standard.