I know Apple is the guru of human interface design, but that is why it is so odd to me that there are so many inconsistencies that even I see and could do better at implementing! ...
What you are forgetting (and those you quoted also), is that UI changes all the time. The main reason Apple decided to go with Unix under the hood and their own graphics on top is they realised that the UI part of any OS is flexible and fluctuating.
They may have wrote the human user interface guidelines, but anyone familiar with their OS's can tell you they did not follow them to the letter even when they were writing them. There likely never will be a "set" appearance and many other groups of designers besides Apple have sat down and tried to codify what should or should not be in a UI with mostly the same shifting incomplete results.
Those guidelines were mostly written by a guy named Bruce Tognazzini who worked at Apple in the early days, but he's just a smart guy who knows a lot about design. It's not like his word is god or anything. He recently wrote an article about how Apple's UI's are too "flat," that they don't scale well and he's really mad at them for the direction they are going in.
Now you may agree with him or with Apple or neither, but there is no one "right way" here. IMO his latest writings read like a bunch of
petulant nonsense despite the fact that he is a certified card-carrying genius. No one is right all the time.
Another "genius" pushing back against Apple UI decisions is John Gruber of Daring Fireball fame. He is leading the charge that "click-through" is somehow a horrible horrible thing and Apple should stop doing it. Again, to me, (and others of course) his argument is full of holes and total BS but being against click-through is very popular at the moment, so you will see a lot of writing around the web basically miming his ideas (which he actually borrowed from others anyway).
I guess I'm going on a bit here, but my point is that there is no "one way" with UI design and even the smartest best designers out there neither agree nor always make any sense themselves when criticising Apple's take on the same issues.