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.