Maybe it is too late to answer but I will try anyway.
The main difference between the two architectural styles are the flow of data.
On one hand, for Pipe-and-Filter, the data are pushed from the first filter to the last one.
And they WILL be pushed, otherwise, the process will not be deem success.
For example, in car manufacturing factory, each station is placed after one another.
The car will be assembled from the first station to the last.
If nothing goes wrong, you will get a complete car at the end.
And this is also true for compiler example. You get the binary code after from the last compiling process.
On the other hand, Layered architecture dictates that the components are grouped in so-called layers.
Typically, the client (the user or component that accesses the system) can access the system only from the top-most layer. He also does not care how many layers the system has. He cares only about the outcome from the layer that he is accessing (which is the top-most one).
This is not the same as Pipe-and-Filter where the output comes from the last filter.
Also, as you said, the components in the same layer are using "services" from the lower layers.
However, not all services from the lower layer must be accessed.
Nor that the upper layer must access the lower layer at all.
As long as the client gets what he wants, the system is said to work.
Like TCP/IP architecture, the user is using a web browser from application layer without any knowledge how the web browser or any underlying protocols work.
To your question, the "hierarchy" in layered architecture is just a logical model.
You can just say they are packages or some groups of components accessing each other in chain.
The key point here is that the results must be returned in chain from the last component back to the first one (where the client is accessing) too.
(In contrast to Pipe-and-Filter where the client gets the result from the last component.)
