> In other words, the writing system being a detailed model of phonetics is not necessarily a good thing.

> No romanization scheme captures all the phonetic nuances of Japanese.

The fact that alveolar and palatalized sibilants both exist as contrasting phonemes is not a "nuance". It will be represented in every writing system that anyone ever puts forward, as indeed it already is.

The only advantage of putting 'si' in a Romanization of Japanese is that it corresponds well to the official alphabetical order of Japan. There is no other reason you'd do it.