I mean if you restrict things enough than any metric is possible. Looking at 500k people (your link) out of 37m (Tokyo Prefecture) or 9m (Tokyo 23 Wards) I feel isn't the best metric.
For Tokyo, I think discussions about population change should be focused on the 23 central wards. Here's a more up-to-date source: https://www.toukei.metro.tokyo.lg.jp/jsuikei/js-index.htm (it seems to be 14mil today vs 9mil in 2016)