Why? What else would you be representing as 'ti'? たちつてと is the related line (e.g. verbs ending in ち become て when you put them in potential form) so romanising them as ta/ti/tu/te/to makes sense.
When you say "non-native speakers" you mean "monoglot English speakers". Hepburn represents the sounds in a way that corresponds to English peculiarities; it's easier to read for English speakers and English speakers only (speakers of non-English languages with Latin orthographies find Nihonshiki easier). It makes sense for teaching materials aimed specifically at an English-speaking audience, but not on e.g. signs aimed at international tourists.
FWIW, I'm a native speaker of a non-English language with a Latin orthography, and while the language doesn't use the English digraphs "ch" or "sh", those are still widely understood and found in loanwords etc.
I was going by my experience of Irish and German, where "ch" has a specific pronunciation that is quite different from that Japanese sound. Having found https://commons.wikimedia.org/wiki/File:Pronunciation_of_CH_... I guess I was generalising too much myself :).
The 50音表 regularity is real and meaningful (e.g. it shows up in verb inflections); any representation that lacks it is necessarily less faithful to the native experience. Whereas the letter-sound correspondence in Hepburn is not consistent in the first place ("chi" for ち is ridiculous to anyone who speaks a non-English language), so the idea that Nihonshiki is somehow less consistent is simply wrong.