I was about to give an answer, then I realised I'd probably misunderstood the question in the first paragraph. You're referring to the "void" areas that can't be traversed, right?
I think that void is in the first category - it's a natural characteristic of the paths of the Shadow World that there are some places that you just can't go, and that sometimes they move. In some cases, it's probably less that the void itself is moving, and more that the paths that you
can travel through are moving, and void is what you have left when a path is removed. Turning a region into void, therefore, is less about hitting the region with the void, and more about destroying (or removing to somewhere else) whatever was there and void is what is left. Certain powerful entities have the ability to manipulate this, and as seen in some of the later Shadow Magic scenarios, it's possible to get the Shadow World to start to overlap with parts of Athla, causing Athla to have some of the properties of the Shadow World. (This is probably not healthy for the planet in the long term - from memory, in Shadow Magic it was described as starting off with Shadow World features starting to appear on the surface, and then the surface starts getting ripped up and pulled into the Shadow World - presumably, this was reversed after Shadow Magic, although the Sunbirth Mountains still showed some of the scars in AoW3).
Anyway, one way to think of it is that while everything is portrayed as a two-dimensional map, like the underground maps, that probably isn't strictly accurate. Two paths that are adjacent to one another and separated by void on the map might not actually be at the same "altitude", for want of a better word - they might actually be separated in a third dimension, or even in a fourth dimension that those traversing the map do not perceive.
Regarding the Wizard's Realm, it might be worth checking with
@Refineus (particularly since I'm largely going off memory here - due to some issues with switching between computers, I don't currently have Dropbox access to double-check the notes and plans), but from what I recall it's essentially a demiplane - it's not a full planet like Athla, but it also doesn't have the properties of the Shadow World. Most likely, it's a region of the Shadow World that the Wizards have used their magic to cut off from the rest of the Shadow World (apart from their own portals), filled with as much magic as they could collect, and reshaped to their liking, attempting to recreate the Circle of Evermore. From the perspective of the protagonists, they don't really know much more than that it's weird, it's separate from both the Shadow World and Athla, and that it's a power source for the wizards with different regions of the demiplane corresponding to different spheres of magic.