People who have come from London and New York City have compared Tokyo fairly equivalently. I agree that the "study" was real science. To compare cities only on the basis of a few items popularly bought only by expatriates is a flawed approach.
Having lived in Tokyo, and having now lived in other parts of Japan for over 10 years, this is my opinion.
Expatriate items are more expensive than most other items.
Tokyo has a higher residence tax, I believe, than most other cities.
Parking is more expensive in the bigger cities.
National health insurance is based on your location, so that is probably also higher in the big cities.
These and other factors contribute to what the average person, not just expatriate, has to pay to live on.
1.5 million yen/month for an apartment. Gee, hard to say if that's tough on the chairman, JerseyBoy, since he doesn't pay for it himself!
You can bet it's not a closet.
I heard that many foreign expatriates (e.g. financial institutions) live at VERY expensive apartment of million yen monthly rent in Azabu, Roppongi and Shibuya.
You can bet those people get subsidized housing, though, and many perks that your average salariman or English teacher does not.