They're probably not, but the point is to defend against a loss of headquarters and all the resources surrounding it,
regardless of the cause. Note that a network partition (where the Bay Area is fine but cut off from communications with the outside world) is functionally equivalent.
There are a number of other scenarios that could conceivably take out all Bay Area offices: nuclear strikes on SF + Moffett Field, wildfires in the Diablo Range that sever all communications, secession of California and following military blockade, large scale protests or civil unrest that do the same, etc. Might as well protect against all of them rather than special-casing earthquakes.