A single layer transparency setting could be applied so that only the top layer is blended. This would be especially useful for lighting/shadow effects. If you were to have multiple shadows cast into the same area, overlapping ones wouldn't blend on top of each other to make the shadow look twice as dark, they would seamlessly blend into a single shadow. Also, if you were to shine a flashlight transparency into the area, it would completely negate any shadows, making the area look brightly lit. Preferably, it could be applied on a per atom basis.