I think big companies see a lot of opportunity in locations outside of Silicon Valley. If you don't care about the weather in the Bay Area, which is quite pleasant, or the other industries around you (be it for business or for pleasure), then you can get an easier commute and a better house for the same salary, which is appealing to some people. (You can also pay people less, which seems to be a strategy used by companies without any Bay Area locations.)

As for how these offices exist; sometimes the team lead is senior enough to move the project there because they want it to be there, and other times a company is acquired that has offices there and there was no reason to move them. (I think Google got their NYC office by buying DoubleClick, for example.)