It's a change in purpose. Nihon-shiki was invented to teach Japanese people the Latin alphabet, with a view to replacing kana/kanji with the Latin alphabet. Therefore being understandable to someone with a good idea of the kana layout was the priority.

Hepburn was designed to teach non-Japanese people Japanese, therefore matching well to European (especially English) sounds was considered more important.

Suggesting Japanese romanise is a fringe position these days, much much more so than in the 1880s or the immediate aftermath of WW2, and making that kind of change is much easier when you have a population going from illiterate to literate than in a modern society, so nobody's seriously considered Nihon-shiki (or its slightly modernised descendent, Kunrei-shiki) a gateway to romanising Japanese for the Japanese for a long time now.

So this is sort of an official recognition that the primary purpose of romaji is for the benefit of foreigners.