I just stumbled upon this statement on the PC-98 page:

The PC-98 computer platform eventually went on to sell more than 18 million units in Japan by 1999, surpassing the Commodore 64 (17 million units) as the best-selling home computer system of the 20th century.

I think this is comparing apples with oranges. The C64 is usually cited as the best-selling single-spec platform, i.e. a model bought in 1982 can still run all the software released in the early 90s. The PC-98 is a series of computer models that, at various points, sacrificed compatibility in favor of technical advancements. On that basis, it is more comparable to the MS-DOS or Macintosh platforms, both of which were better-selling systems than the PC-98 during that time. The PC-98 is "only" the best-selling platform in a - compared to North America and Europe - relatively small market.