As I originally understood it, there are two types of alternate dimensions- parallel, which are similar to the "main universe" but diverged at some point and thus have a different timeline, and "alternate" or "pocket", which are not similar to the main universe. The Field of Shadows was some other strange dimension, but the Kingdom or Dark Mirror universes were parallel timelines.
Now of course we know that the so-called Matoran Universe is really the insides of a giant robot. It's not a universe per se, it's a part of a larger universe. So... what exactly are these pocket dimensions? BS01 says:
Pocket Dimensions are minor universes linked to the Matoran Universe; their integrity is tied to that of the Matoran Universe's and, subsequently, the health of Mata Nui.
This makes it sound like they are, in some way, part of the MU- or, more accurately, Mata Nui.
Is it possible they are actually separate components of Mata Nui? Created by the GBs (or Mata Nui himself?): perhaps they're just sealed-off components of Mata Nui's structure, or more satellite bodies such as the Red Star. Or maybe they are alternate dimensions, and Mata Nui actually extends into alternate universes and is more like a separate universe than we might think?
Perhaps all this is already known or hypothesized, but I haven't read anything on the subject.