One key difference that jumps out at me between various cities in Japan and Vancouver is that the COL seems significantly better in Japan. When I visited Vancouver I couldn't afford to stay in or even near the city, I had to find a place about 20 minutes away and even then it was pricey. Whereas in Japan I had no problem finding affordable stays in city centers in all of the major cities I visited, including Tokyo.
I will admit my ignorance here however and acknowledge there are likely myriad other variables at play here that I'm not considering.
As a visitor, it's probably impossible to know the real cost of living is in different areas, because you're not employed locally, paid local wages, or paying rent and utilities. You are a foreigner with foreign money staying in hotels.
Affordable to you or affordable to the locals? The yen has devalued a lot in the past decade or so, giving foreigners a lot more spending power in Japan and causing the current tourism boom and backlash.