As someone intimately familiar with this topic, the article here is mostly correct but gets a lot of the small details wrong.

Probably the most important missing part here is the reason non-Hepburn systems like Kunrei stuck around for so long: they were designed to replace the Japanese script completely. This sounds outlandish today, but they were invented during the early Meiji years when Japan was adopting Western innovations and abandoning ancient traditions at breakneck speed. And because their target was thus Japanese people, not foreigners, they didn't need to worry about English phonology.

Incidentally, the Chinese pinyin system was also designed to replace Chinese writing, and Mao came quite close to abolishing Chinese characters entirely during the Cultural Revolution. Which also explains why it uses letters like x, c and q in ways that English readers find wildly unintuitive.