For whatever reason. Saving a png with an alpha layer actively deletes the pixels that were made transparent by the alpha layer.
I'm well aware the point of an alpha layer at least traditionally is transparency. But if I save a PNG in Photoshop with an alpha layer, I can open that image in any editor and enable or disable the alpha layer at will in order to show the parts of the image that were made transparent. In Affinity Photo, when I save with an alpha layer, any pixels that were made transparent are actively deleted from the main layers, meaning that there is just an empty black spot where the alpha layer is if you decide to disable the alpha layer.
This makes absolutely no sense given Photo 2's emphasis on non-destructive editing. I understand that it might save on file size, however for that kind of decision it should be at the very least in the export dialog. I need to keep the data that was made transparent by the alpha layer, I don't want it deleted, I just want it hidden until I choose to unhide it again. Unfortunately yet another thing that puts Photoshop ahead for the moment, that I'm hoping is fixed.