According to the "salary buying power" section, Silicon Valley's cost of living is 23% higher than that of NYC. Having lived in both, I'd be very surprised if that's not actually the wrong way around.
Even the central part of SV is quite cheap compared to NY for some living profiles. Buying a house is expensive, but renting one is relatively cheap. Going rate for a 2-bedroom house in a tract development in Santa Clara is maybe $1500/mo, while even out in Queens you're not going to find a house at $1500/mo.
I'm not sure where they got the $2250/mo average apartment price from; that seems high. Perhaps it's skewed as a mean, by a few really high-end apartments? It'd be interesting to see how the median compares.
A lot of the statistics are questionable, most certainly including the average apartment cost.
For the creatives who stay in SF, the other comment by hugh3 is correct. Most live where you'd expect: the mission, the tenderloin, 6th and Market, etc. Oakland is also popular but not as much as the people who choose to live there make it seem. Artists in SF aren't necessarily living in squalor (or at least any worse squalor than hipster web programmers). My neighbor made a good living painting cartoon robot monsters.