This after over $2 billion dollars spent so far, and after a vulnerability review halfway into construction (why did it wait until then?), Fred Clarke said "We already had a very safe building. Now we probably have one of the safest buildings in the world." [1]
Is it ideal? Of course not. But it is far better than ignoring the problem as was done in Miami, where a college’s pedestrian bridge collapsed over a roadway (after possible failure signals were ignored), killing several people on the roadway below and a construction worker.
Yep, never said it was bad. But the cost of this transit center is absolutely enormous for what it is -- a glorified bus station and park. There aren't even plans for BART connectivity, and the cost doesn't include the pricetag for MUNI metro linkage.
I'm not a California resident, and don't have the bandwidth to perform this, but you might consider using Muckrock.com to dig in with FOIA requests to determine what the story is with regards to the cost, budget, engineering deficiencies, etc. I'm happy to gift you requests to get this done (there is a small cost).