I rode Stage Gulch once and will likely never ride it again -- I agree it's a very unpleasant route for cyclists. But the list above includes "Highway 116," and Highway 116 covers a lot more ground than just the Stage Gulch section, much of which is more well-traveled by cyclists. So its inclusion may be very much based on the level of cyclist travel it sees.
Market Street is #1 on the list -- in part because there's a lot of chaotic car traffic on it, and in part because it's perhaps the most heavily trafficked bike route in the city. Riding on Market, I feel at least as safe as I do riding on Geary, but Geary doesn't even make the list because the level of bicycle traffic on it is not nearly as high.
Because the numbers we're dealing with here are so low -- the "deadliest" road in the Bay Area averages only one death every three years -- it seems like the amount of cyclist traffic, along with the length of the roads in question, are going to end up being very significant factors in determining the road's supposed dangerousness.