I think you're just not being clever enough in replicating with two layers what you could have done with three. The only thing I can think of this could be used for is clearly having an additional element beneath a low opacity hitcircle, which can easily be replicated with that element being in a lower opacity on the overlay layer. As an example, with a star in the middle of the hitcircle, one being beneath the color layer and the other in a low opacity on the overlay.
Opacity does work slightly differently depending on what layer is the top one, but it's such a minor difference and doesn't quite justify such a request.