There are 2 things being discussed here:

1) people being confused by the back button because they don't realize it will always pop the current view of the navigationstack, which is systemwide.

2) the fact that the back, menu, search and home buttons are dedicated hardware buttons.

Explaining how 1) works does not mean that 2 is not broken. Personally I find 2 to be the interesting discussion.

Seeing how these hardware buttons are being changed to be a dedicated part of the Galaxy Nexus' touchscreen, and how not all vendors actually put all 3 buttons on there, it's not too hard to argue that something about the hardware buttons is at least flawed, if not broken.