Pile foundations are impractical for much of San Francisco founded on bay mud (bedrock hundreds of feet below surface). There're other practical solutions - including soil improvement, micropiles and/or raft foundation - that have been proved capable of supporting highrises.

On a different note, a settlement (even differential) in excess of one foot is expected for a significant fraction of building stock in SF in the event of a "design-level" earthquake.

The tower is reportedly 6" out of plumb. Over its 600ft height, that's 0.08%. For perspective, it is generally accepted that construction tolerances will result in a building 1/500, or 0.2%, out of plumb at the time of erection.