You're right, what I had in mind was 2, although a bit more general; I think there have been similar kinds of inconsistency in the Mac UI since the beginning, in various forms, almost always intentional.
So I think it would be wrong simply to say "the UI has gone a cliff, they've just thrown away their own HMI guidelines." You can certainly dislike what they've done (and I do dislike it!) but they at least have a somewhat logical goal in mind -- in this case, making the corners neatly fit various different kinds of window content.
Having said all that, there are also some real bugs and unintentional glitches, like scroll bars and other widgets not fitting correctly. I'd agree that seems to be happening more often in recent years, so their quality control has gone downhill.