For what it’s worth as a long time learner of Japanese, none of these ambiguities has ever confused me nor hindered my ability to be perceived as natural to native speakers, so I think that this ambiguity is not such a big deal.

To me, Hepburn’s strength relative to the old government romanization is that it increases the likelihood that an English speaker will make approximately the right sound when reading some Romaji, and that people seem to prefer it in general.