As someone who also “deconstructs” adventure games, I would really be interested in what the creator of the Puzzle Dependency Chart™ leaves out specifically from them.
The thing is, and maybe I just go too much over the top probably, that when I deconstruct one, I usually write down every single piece and interaction (or most of them, I suppose) and their outcome from start to finish.
In the last one I wrote, I analyzed the adventure game Technobabylon and “went berserk” writing down also every piece of information about the background story, the game world and characters.
I know that this is probably too much for Puzzle Dependency Charts’ sake, but made me realize clearly that, while Puzzle-wise, Technobabylon is made of different “closed compartments”, it had a huge amount of narrative detail (love it or not, that is).