Did you know that it could take so long when you first started your PhD in Korea? Could this be one of your reasons to move to Japan?
My decision to start my PhD in Korea was under very different circumstances. I was studying a totally different field (automata theory, so closer to mathematics than ML) where longer PhDs were normal, I was used to the US system, I wasn't working or married, etc. I expected it to take ~6 years when I started.
I basically had to choose between living in the Canadian countryside, Helsinki, or Seoul in order to be in a lab studying what I wanted. I was already pretty into Korean culture (I minored in Korean in college, studied abroad there, and was a serious StarCraft player) so that choice was easy!
When I started looking again, I knew I wanted a shorter PhD (especially since I had a masters and industry + industry research experience), so Japan was pretty attractive.
I will admit that I think 3 years is a little short to make substantive progress outside of machine learning, so unless you come in with a lot of research experience and a good idea of what you want to work on, I think a longer PhD would be beneficial, but the opportunity cost is so high that it really doesn't seem like a great option on paper.
One aspect worth calling out as a huge plus of Japanese national institutions which the author didn't disclose is funding for compute is much better than what one would get from a Korean institution (e.g. the author's school runs one of the biggest GPU clusters in Japan).