When using the layer window to inspect and manipulate mask overlays, the colors next to each mask plane can differ quite dramatically from what's in the image due to the alpha being used in the image but not the layer window.  It may be hard to get this right, as what the alpha does depends entirely on what shade of grey the image "under" the overlay has, but I think we could find something better than ignoring the alpha entirely (maybe half white/half black?) to reproduce those colors-with-alphas in the layer window.