Overlay Layers Opaque over Transparency?

I have a file with one Overlay layer and several Normal layers beneath it. The normal layers are drawings and have alpha transparency. I'm using the overlay layer to modify the colors of all lower layers at once.

Here's my problem: I need to export the normal drawing layers individually, with the overlay applied, preserving the alpha transparency, but the overlay appears opaque ( as if it were a normal layer) anywhere it overlaps a transparent area of a lower layer. Shouldn't it be transparent in these areas as well?

This is preventing me from exporting transparent PNGs since the overlay is basically creating a background. I've tried merging the overlay onto the alpha layers individually, but this just causes the same issue.

This is an artboard document by the way, which I understand can have different settings and cause problems. Is there any way I can make overlays appear transparent over transparency as they logically should?

- Matt