Hi -
I don't know about engineering, but I know a little about lab-based PhDs here in Japan and it's not good. The supervisor-student relationship here seems to be even more exploitative, although these are just anecdotal observations.
I'm humanities, and PhDs from Japan in humanities aren't regarded well. It might be different from science. Some do it though, especially if they are on the MEXT government scholarship, but that is really hard to live off these days...
On the other hand, Japan is a great place to be for a few years!