The problem isn't the data itself. The problem is how the data is interpreted, unfortunately. Lifestyles don't map properly between cities, countries, and cultures. In the US you need a car in a lot of cities, you might want/expect a "suburban" lifestyle (large house, garden, etc). Healthcare might be an overlooked cost. Taxes and social contributions (pension, etc) might affect all these numbers. It's incredibly easy to just look at the raw data and go "X is more expensive than Y" but in reality the situation is much more nuanced than that.
Also, as I said, Tokyo really isn't one city, it's a huge gigantic collection of multiple cities with an incredible public transport system that really doesn't make you feel like you're not living in a "city center" even if you aren't in one. I can step out of my house and be in a "downtown" area in less than 10 minutes by just taking one train and there is one train every 2-3 minutes.
If anything, I found https://www.numbeo.com/cost-of-living/ usually has a much more nuanced breakdown of actual living expenses across cities, although their rent metrics also are quite incorrect because the way rent and housing space is measured in Japan doesn't quite fit a western standard unit of measure.
I'll preface this with: A lot of what you're saying resonates a lot.
That being said, I think what you're saying about being unable to compare rent prices more or less boils down to "ceteris paribus". Of course, not all else is equal, but it's still relatively meaningful to compare rent statistics, especially considering that it tends to be a dominating cost term. And, directionally speaking, the figures they quoted ultimately led them to a conclusion that I believe is right.
Also, as I said, Tokyo really isn't one city, it's a huge gigantic collection of multiple cities with an incredible public transport system that really doesn't make you feel like you're not living in a "city center" even if you aren't in one. I can step out of my house and be in a "downtown" area in less than 10 minutes by just taking one train and there is one train every 2-3 minutes.
If anything, I found https://www.numbeo.com/cost-of-living/ usually has a much more nuanced breakdown of actual living expenses across cities, although their rent metrics also are quite incorrect because the way rent and housing space is measured in Japan doesn't quite fit a western standard unit of measure.