When composing a mask from multiple layers, they need to use an appropriate blend mode. If it's left at 'replace' the layer on top will replace the one below. On more complex models I often create folders for the different material IDs with the corresponding mask. Other than vertex color, I like to use different materials…
As far as I know the "deep" exr stores records of multiple hits a ray-tracing ray does when it goes through a scene for a single pixel . like two intersecting clouds and a wall . I t stores samples of cloud 1, then when it goes through and hit cloud 2 and then the wall/object behind . it can record layers and layers of…