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Deep data has many benefits. It allows artists to control complex layering in 3D space. You can re-project color information later should it change and adjust it using compositing nodes. You can apply better quality camera effects like depth of field and even composite objects into something like a fog field or other volumetric effect without re-rendering. Or maybe you need to nestle a baby bird into some tall grass surrounding them, you can do that with deep data.

For quality, you can use the render option for deepshadowerror to control the merging of samples where larger values merge more samples but may introduce precision errors in compositing.

Note in the image directly above, opaque objects cut out the object behind them while transparent objects (objects with partial presence) can reveal what's behind them like the blue ball behind the yellow wall. (Since the wall was rendered at the same time, the blue ball color is baked into the wall.) Note that the green ball, despite being opaque, does not cut into the yellow wall, this is because it was rendered separately with primary visibility off and then merged in Nuke along with the floor that has the shadows baked in.