Each layer might only have some subset of the objects in the scene, but the lighting on those objects might still use the indirect contribution from all other s

Each layer might only have some subset of the objects in the scene, but the lighting on those objects might still use the indirect contribution from all other scene objects. So for example if your scene has objects A, B and C, you might break it up into a layer for each. Then to render the A layer, your primary rays would intersect with object A only. But any secondary/indirect rays would intersect all of A, B and C, so you'd still get the correct global illumination on object A. Breaking it up this way just makes things easier to adjust in compositing. Also the indirect for each layer often will be rendered as a separate pass entirely so it can be dialed in comp independently, or regenerated if the scene geometry changes. It's also important to understand that almost all the lighting in feature rendering is incredibly faked and not physically-correct at all. This is particularly true in animated movies. It's just important that the end product looks plausible, not that it's academically correct. Global illumination helps add a bit of realism and nuance, but its contribution to the final image is pretty subtle, especially between objects that are far apart. Nobody would ever notice if the indirect lighting wasn't perfectly correct in all but the most close-together objects. So a lot of the time it won't be re-rendered if the scene changes slightly, as long as it still looks decent. Without global illumination, to get the illusion of light bouncing between objects lighters would have to place spot lights for every bounce they want to fake. Like a ground light pointing upwards below a character to fake light bouncing off the ground etc. People really used to do this, and it's a real pain. This is the "time consuming manual lightning" they talk about. Global illumination tools make that process automatic and are able to get much richer light interactions than anyone could set up by hand. But they're still just tools. And like any tool, artists will break them apart and use them in whatever hacky way they need to get a shot to look right. Getting the exactly correct solution to the rendering equation is just not important.