No, layering just means generating multiple renders for a given shot, which can then be combined to create the final image using 2d compositing software such as Nuke. Full 3d renders are always going to be much slower than just doing image manipulations in 2d, so it is much more efficient to iterate by making adjustments in 2d than by re-rendering everything from scratch every time you need to make a change. Additionally if just one element in a shot changes, say a character's animation changes, it much more efficient to just render the layer for that element again than to re-render ALL the geometry for the entire shot. Each layer may still be rendered with full global illumination and whatever other fancy lighting is needed.. the layering just makes it easier to iterate in individual pieces of a shot.
In feature animation things are changing and being adjusted constantly. Each shot is worked on by many people across multiple disciplines, all of whom do many, many iterations to hone in in the final shot. So the entire production pipeline is designed to make handling changes as efficient and easy as possible. Look at the amount of processing resources disney used for this movie.. I can guarantee you they are cutting all the corners they can and maximizing efficiency wherever possible. Doing a single monolithic render every time something changed would be extremely inefficient.
That said, there are a few studios that do produce complete final frames in-render. Usually places that write their own renderers in-house and therefore have a sort of macho academic attachment to showing off how much their renderer can achieve out of the box. Blue Sky is this way because their whole pipeline is designed around their cg studio renderer. Anecdotally I have heard that Pixar did everything in renderman for a long time but more recently they have started using more of a compositing workflow since it's so much more efficient. So it's possible that disney may be this way now since they have this fancy new hyperion renderer they wrote, but I certainly wouldn't bet on final frames all being done in-render.
But the layers aren't independent at all, so how is it done? For each small change you show have to resolve the full rendering equation (although that should be easier given small changes). So I understand they may want to use something like that for quickly visualizing changes, but I can't see it used for actual rendering.
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.
In feature animation things are changing and being adjusted constantly. Each shot is worked on by many people across multiple disciplines, all of whom do many, many iterations to hone in in the final shot. So the entire production pipeline is designed to make handling changes as efficient and easy as possible. Look at the amount of processing resources disney used for this movie.. I can guarantee you they are cutting all the corners they can and maximizing efficiency wherever possible. Doing a single monolithic render every time something changed would be extremely inefficient.
That said, there are a few studios that do produce complete final frames in-render. Usually places that write their own renderers in-house and therefore have a sort of macho academic attachment to showing off how much their renderer can achieve out of the box. Blue Sky is this way because their whole pipeline is designed around their cg studio renderer. Anecdotally I have heard that Pixar did everything in renderman for a long time but more recently they have started using more of a compositing workflow since it's so much more efficient. So it's possible that disney may be this way now since they have this fancy new hyperion renderer they wrote, but I certainly wouldn't bet on final frames all being done in-render.