One thing to note is that, after I submitted the final draft of this article, the Japanese government ended the MEXT university track or is at least planning to. There was a memo, but the status is not clear.

Anyway, I had a great time doing my PhD this way, and generally I recommend that people work before a PhD and try to work during it (if you are in CS). It gives you a lot of freedom and, at least for me, it is very helpful to have more than one pipeline of work at a time so that when one slows down (as it inevitably does in research), you can draw on the other.

One small pushback: The author writes, "the Japanese PhD system pushes you to graduate in three years." This applies in some programs and some fields, but is by no means universal. In the graduate program where I used to teach (I am now emeritus and no longer supervising students), the steps leading up to the Ph.D. and the expectations for the thesis made it practically impossible for students to finish in three years, especially if they continued to work part-time. This created particular challenges for foreign students on MEXT scholarships who had to work out other ways to support themselves and renew their visas while they continued to write their theses.

  Doing a PhD is difficult and isolating, which is exacerbated by being an international student in an unfamiliar country. And so, while I overall very much enjoyed my time there and have freely recommended it to many people, the decision to pursue a PhD in Japan should always be considered carefully.