Isolation and centralization is useful for the corporation; they have more control over physical security, can manage it so employees tend to interact only with other employees, and it costs a lot less to have space for 12,000 employees off the interstate than to have them downtown (if Silicon Valley towns even have "downtowns;" I know far-flung Miami exurbs usually don't.)
Cupertino did have a downtown along Stevens Creek and De Anza, but the area changed significantly in the 1950s and 60s when streets were widened and DeAnza College was built. Cupertino certainly doesn't have much of a downtown now.
Sunnyvale didn't really until they started building a clone of Santana Row that went belly up with the housing crash. Well I guess Historic Murphy Avenue sort of counted.
As a former Apple employee I cannot disagree more. Everyone at the mothership needs more sunlight, not less.
I can't even remember how many days I got to work when the sun was coming up and left as it was setting, or after it set. It was like a perpetual winter.
