Kunrei-shiki is intended for domestic Japanese use. That's why it results in spellings that don't make logical sense for any Latin-based phonology. It's too focused on round trip unambiguity at the cost of phonetic clarity for non-Japanese. My big peeve is the company Mitutoyo using K-S, which everyone mispronounces because they don't know it's a poor transcription of "Mitsutoyo".

Oh! That's fun to learn, given where I am from (not Japan) we all call it "Mi-chu-toy-o". A combination of misunderstanding and dialect.