See if you can match the Hanging Rat elevator with its other end in Deep Caverns (dc-tw).
Yes, I also thought that it was the same Elevator shaft. However, they are very far from each other, they cannot be connected without the intermediate connection locations, which, in turn, does not exist.
PS. The "LowerCaves" are above Caves and probably above Underpassages as well. Look at the GMS exits to see how they are laid out.
why in this case they are called the "Lower caves"?
In this sense, my view of the topology is more logical, isn't it?
I always imagined the dungeon so that with increasing depth the origin of the cavities becomes more natural than artificial.
In any case, I think the arrangement of the layers is not so important. Because moving between them is not wasting time and no other game resource. What is important is the location of the blocks relative to the transitions in other blocks at the same level, it's important for navigation.