When confronted with expensive coffee, I remind myself that other people's addictions are far costlier!
That said, we need to remember that these surveys are totally pointless, because they measure the cost of living for expatriates; i.e. for people who often don't "get" the local society and live in small social bubbles. Furthermore, it's bound to be culturally schewed; I'll bet the habits of Japanese expats in NYC are factored in the city cost of living to a much smaller extent than those of US expats in MOW.
You can have a perfectly decent coffee at a perfectly decent cafe in ATH for 2.5 Euros (incl. table service) but "rubbing shoulders" with ministers and shipowners comes at a price, one that can easily exceed 5 Euros for a cappuccino...
Similarly with PEK. I've not been there, but I've been to CAN, and coffee in the local coffeeshops/small chains or even the odd Italian restaurant costs far less than the $6.28 charged by *$ et al.