When you're inside, everyone you encounter will be an Apple employee or contractor and not random people off the street. Which could be a problem for Apple, because there are tons of tourists that come by to have their picture taken. You really don't want these people bugging your employees.
And the cafe is completely open to the courtyard with no badging. You can't have an open campus and have the cafe open to the outside without a controlled outdoor space.
And it adds to the whole idea that this is an exclusive group of people. Which I always felt working there as a contractor. You're in but you're not as in as other people. I'm sure this is a very deliberate thing and it does work on many people.
Anyway, I've always wanted a house where you be in nature but be just as secure as you are in your house. I was in one house where the interior courtyard had trees and all the walls were glass inside. It was awesome. Sleeping outside would be just as safe as sleeping inside, except for the stray ninja attacks, of course.
I, too, worked as a contractor at Apple for a while and it was a little depressing how few people actually used the interior courtyard. Occasionally I would have my coffee out there to enjoy the sunshine, take some notes and people watch, but mostly it was an empty space that collected dead leaves and dust. My impression of the cafes in every building is that they were slightly subsidized to encourage employees to take their coffee break without leaving (which has the added benefit of avoiding potential leaks). Every aspect of life at Apple is highly controlled (to a degree, some areas less than others), so it isn't surprising that this extends to the cafeterias, stores, cafes, parking and even the printers.