That page is very outdated. More than 4 years old! Not even close to the current prices!
Also, just for your information, the japanese yen was continuously deflated in US dollars in the last 2 years or so. So even if it might seem from the US that this is cheap, the prices were soaring during the last 2-3 years in japanese yen.
So if you were unlucky enough to have a japanese salary in the last few years (as the locals mostly do), chances are that your real wages got continuously deflated.
Tokyo is actually much more expensive than other huge asian cities like Shanghai or Bangkok (denominated either in JPY or Remnibi, Thai Baht). That was also largely the reason for the LDP's abysmal election results this last Sunday.