I think the title (and the article to a degree) is misleading. Something like "Japanese bureaucrats finally plan to update severely out of date official romanization scheme" would be far more accurate.

The examples in the top table make it clear, I've never once seen judo romanized as zyûdô, it's always jūdō. Out of curiosity I asked a native Japanese speaker and although they could figure out what word it was they had never seen the former romanization either.

The title also makes it sound like a new romanization system was just created, when in fact it's just modern Hepburn, which is how everyone other than the Japanese government has been romanizing Japanese words for ages. The article does mention Hepburn to be fair, but then it makes it sound like the proposed changes are something new and not the de facto standard.