From a quick google search, it appears 20,000 of Google's 60,000 or so employees are headquartered in Mountain View, and it is widely considered the company's "headquarters." I'm not sure it's apt to think of it as an exception. And it's in the process of being rebuilt, which can be understood as a doubling down on this approach.

Perhaps. However, calichoochoo implied this at least true of one more office, as it "continues to make the wrong large decisions by putting their offices in the middle of nowhere, miles from any real place, surrounded by acres of parking". This seems to only apply to mountain view.

FWIW I agree; I can't think of a place I'd like to work less than the bay area. There's no good option for living there, let alone commuting.

So it's better to pull an Apple and completely cannibalize a city by building a giant spaceship in the middle?

For smaller offices it makes sense to have them in the middle of the city, for something as large as their Mountain View office, it'd be a huge mess inside a city for someone of that scale.

And you're forgetting the fact that the headquarter has been growing naturally over the years, so if they had indeed started in a city, they would've probably had a really hard time expanding.