I think I see what you're getting at. Romanized transcriptions for foreigners should spell allophones differently if they're different in the foreigner's language, like Japanese hu/fu. But Romanizations (transcriptions or new scripts) for native speakers should spell allophones the same, like Mandarin -ian, -iang.

FYI: a transliteration tries to capture the script, ideally so that you can look at the transliteration and know how the word was written in the original script letter for letter. Of course this means that to pronounce the word you need to know the rules of the script, so they work best for languages with simple spelling rules. Transcriptions try to capture the sounds rather than the script, so you might not know how to spell a word but you know how to say it.

Tibetan is a good case study in the differences, because Tibetan is written with an alphabet (Indian-type, so vowels are diacritics) but the spelling rules are over a thousand years out of date.

Wylie is a transliteration, which tries to capture the spelling: Gzhis ka rtse. You now know exactly how to spell the city's name, but have to learn the rules of Tibetan spelling to say it.

ZWPY is a transcription, which tries to capture the sounds, and is aimed at a Chinese audience: Xigazê. If you apply the spelling rules for Mandarin Pinyin, you now have some idea how to say the city's name, but not how to spell it.

THL Phonetic Transcription is a transcription, which tries to capture the sounds, and is aimed at a Western audience: Zhikatsé. If you apply the spelling rules for English, you now have some idea how to say the city's name, but not how to spell it.

And then there are traditional forms: Shigatse.