This is basically a case of the government removing a rule that almost nobody, including them, was really following. I guess they had it written down somewhere to use Kunrei, but like TFA says Hepburn is what's used virtually everywhere.
So, whatever system one might expect ought to be truer to the source language, the Anglicized system is the one that current native speakers find most familiar.
So, whatever system one might expect ought to be truer to the source language, the Anglicized system is the one that current native speakers find most familiar.