Just because something is not immediately instinctive has nothing to do with it being intuitive as they are two completely different things. If you were to use this new layout for a year and then they changed things back to the old way and you were now executing the new movements as instinctive movements, would the old way be any less intuitive since it was no longer instinctive? By your examples it would have to be. The one time I tried Android, everytime I wanted to activate the screen I instinctively reached for the home button. It had a different home button so I was always just hitting the shell of the phone. It's home button was no less intuitive in usage, but instinctively it wasn't as natural for me after having been used to an iPhone for years.
As for going to the corners, the screen size was kept small to reach most of it easily with one hand, but not all corners can easily be reached so utilizing them is not the most efficient for one handedness and why layouts were chosen certain ways. I know I have little issue reaching the corners with my one hand, but I am the only one in my family that can easily do so. If instinctively reaching for the corner, their thumbs almost naturally fall onto the new done button. Sometimes ergonomics works against some of us.