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... the cities of Antioch west to Martinez are under threat along its shoreline, and we could have flooding threats in the Carquinez Strait, San Pablo Bay and possibly even the piers on the eastern shore of San Francisco.

I don't think it will come to that, causing flooding to the piers of SF. But if, just if, it came to that... keep in mind that SF Bay waters are just a couple of feet below street level at some piers at high tide. If water came over the Embarcadero Street surface then it would cause flooding into the BART/Muni subway tunnels which thousands of people use daily. I can imagine that authorities would evacuate the tunnels if they know a water surge is coming. Nonetheless, it would cause major damage to the subway tunnels (Muni tunnel is second level down, BART is third level below street level and dips under the Bay).