They probably have something to do with that. At the moment, for Japan has a tiny handful of iron mines [0]. So if they want to produce a steel widget, they have to justify someone transporting the iron either through the Chinese mainland or up the coast, past a lot of people who are learning to do wonderful things with steel. They import a lot of coal from Australia but China has relatively easy access overland from provinces like Inner Mongolia.
I'm not sure how much of an advantage they gain from having very easy port access by virtue of being an island (probably quite a big one, I assume). But it is hard to accept they wouldn't be having a much easier time if they had easy access to something like the Saudi oil fields, the US oil fields, the Chinese coal fields, etc etc. They are a long way away from the good sources of natural resources.
And they struggle to be self sufficient in food in the first result I found [1]. That is pretty different from somewhere like the US. There is a real risk of war in East Asia, so I imagine they'd be quite uncomfortable with that.
They have completely different resource-use problems than the economies that are larger than they are. The idea that the US would have to exert itself to be self sufficient in food is rather weird, as is the idea that China would struggle to justify transporting resources to the country from Mongolia, etc. It is obvious to me what could be done with more people in the US or China. In Japan there is probably something, but it does require actual ability to find instead of just "dig more, grow more, build more, forge more" that their competitors for the best-economy crown can manage.
Japan needs transformative technological improvements to grow. The US needs warm bodies. China needed to stop the Great Leap Forward and put competent leaders in charge. The Japanese challenge is much greater.
[0] https://en.wikipedia.org/wiki/List_of_mines_in_Japan
[1] https://en.wikipedia.org/wiki/Agriculture,_forestry,_and_fis...