To confuse things a little further, once you differentiate layers and hierarchical levels, there is I think an important point that may not be immediately obvious (it took me a while to wrap my head around initially).
I have frequently seen projects exploring hierarchies in classical HTM by sending the output of Temporal Memory from one region as input to Spatial Pooler of the next region, and so-on, forming the levels of a hierarchy. However, there seems to me to be a flaw with this approach, since the primary function of SP isn’t to increase abstraction, but rather to fix sparsity while preserving semantics. It doesn’t have a feature-binding property to it.
With that in mind, we must conclude that the actual logical boundary between any two hierarchical levels should in fact be located within the layers of a single region, rather than in the connections between regions. HTM theorizes that each region is internally forming stable object representations from its streaming input. This process is where, I believe, abstractions are being formed.
I am of course starting to move into the area of “Tangential Theories”, but I think this is still relevant to your original question (since it shows that there may not be such a clear physical line differentiating “levels of a hierarchy” from “layers”). In terms of SMI, this would be the process by which activity in the “Input Layer” forms representations in the “Output Layer” capturing the proper semantics of the object (i.e. semantically similar objects should have proportionally similar overlapping bits in their representations).
If we assume that this same process applies to both sequence memory and object recognition, then a simpler way to visualize the concept would be to take the activity from Temporal Memory and feed it into this process to form stable outputs that represent sequences (or parts of sequences). This was referred to in the past as Temporal Pooling. Visually, a 3-level hierarchy could be depicted like so (assuming SP between regions to fix sparsity):
Now obviously HTM theory currently has more than two layers involved in SMI, but these are still the important two conceptually for communicating my point. You can see that the transition from the input layer to the output layer within the same region is actually the logical boundary between hierarchical levels (not the transition from the output layer of one region to the input layer of another region). I think it is this architecture that supports the less traditional forms of hierarchy to be assembled.