Is it really 100% in SF? That strikes me as high -- even in a lot of European countries it's not a full 100%.
Anyway: considering what they do and where they do it, I don't find these numbers high at all. I would be shocked if they didn't have at least a couple engineers making over $200K in actual cash compensation if they're working in the Bay Area.
Overhead doesn't scale linearly with pay. Once you're into 6 figures, it's definitely not equal. I'm guessing much more like $150-200k per employee in compensation.
Taxes, health care, other insurance (disability, etc.), and other benefits (401k, etc.) are a significant fraction of the cost to employ someone. These things are not cheap.
The standard overhead is (I believe--correct me if I'm wrong!) anywhere from 25% to 100%, depending on your base salary and how competitive the benefits package is.
Employer taxes, standard benefits (health, vision, dental, etc), extra benefits (like free food, budget for books, and other niceties), and office space.
Anyway: considering what they do and where they do it, I don't find these numbers high at all. I would be shocked if they didn't have at least a couple engineers making over $200K in actual cash compensation if they're working in the Bay Area.