I have been rendering pngs out of Lightwave with background imagery in the color channels, and an alpha channel for just the objects.
In my comp I duplicate the footage layer, and then on the bottom layer apply the Shift Channels effect, and set the alpha to Full On so I can see my background.
Now I want to run some masks on my backrground layer, but the Full On Shift Channel ingnores all my masks.
I can work around it by doing the masks on a new layer above the BG and telling it to take the alpha from that, but I would rather keep things tidy and all on the one layer.
Is there a different way to tell a layer to not use it's built in pixel alpha info, and look at it's masks?
It works as it always has. Unless explicitly referencing masks in their code and UIs, effects use the source Alpha and that is before any masks. You'd have to pre-compose or indeed use mattes as you already discovered.