Hi Eduardo:
Many programmers refuse to document almost anything and expect the code to speak for itself. Or they throw random comments throughout their code that don't help elucidate things. The nice thing about most Elisp code is that the inputs and outputs of functions are often pretty well documented, since people learn from many good examples. I support you in wanting to document and explain things very clearly for your readers. For most people, Hyperbole is extensively documented down to the function-level. But you want an 'atomic'-level description of the internals of Hyperbole which I think would be useful to only a very small population.
Good programming is about producing and layering clean abstractions that sometimes must mask internal complexity and expose only the interfaces necessary for use (could be a UI, an API or a class abstraction). It's not turtles all the way down as the 'physics' of different levels of implementation varies. Hackers do build from lego blocks; they don't spend their time trying to deconstruct everything just to get comfortable with every component they use, in general. If you want to spend years trying to wrap your mind around something a bit complex then read The Art of the Meta-object Protocol many times. Then, if you survive, come back to Hyperbole and its call tree will seem simple to you :-)
Seriously though, I get that you learn and document differently than many other people, so just do your own thing, your own way. I am reminded of the Hudsucker Proxy where the 'rube' is derided for his stupid idea until later it turns out to be one of the most profitable inventions in history. Maybe the rest of us just can't see what you see because of the way you express it, though if we could, we would be enthralled. I know a bit what that is like!
Best of luck,
-- rsw