You are right, that is the way he wants the project to look like.
Remember his talk "Architecture: The lost years", the architecture should describe its intention(And what better than a Use case?).
At the beginning I was also a bit confused but if we think about it BDD, the philosophy wants to make sure we make understandable software.
I watched the video a couple of times and I probably will again, because it is a new concept and requires study.
For me the most important part and more challenging is creating the plugins for the other modules, he talks about a request and response model needed in order to keep the surrounding layers such as front end and database, completely independent from the software.
The final goal of this is that our software can easily replace any addon such as a database or a UI.
Just one more thing I want to mention, I think you are maybe interested.
In this interview at the end, he reveals that his next book will be all about this new methodology we are discussing now.
Update
I see in the comments you are talking about calling packages with names such as Boundaries, Interactors...
This is completely ok, in his book clean code that some developers use the name of the pattern in occasions to name the Classes or packages... That is correct, because it is technical terminology that developers should be familiar with. In the same way you know that a class is a builder or a factory by reading its name or package, you can know what interactors or boundaries are.
That is correct according to clean code.
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