It helps to look at Hong Kong: similar to SF scarcity of land, excellent public transport, high population density and skyscrapers everywhere, yet it's even more expensive to rent than in San Francisco.
The way I see it: if living in San Francisco is 3 times "nicer" than living in location X, so the rent is 3 times higher. Changing zoning laws does not change the pricing, it simply changes how many people will be living in SF, but as long as it's "3 times nicer" than X, it will continue being 3x the price.