I agree with you, especially with the "depending on the transliteration system".
There have to be several transliteration systems, I can't use a Latin transliteration system from Thai when I am using the Greek or Cyrillic alphabet and I have to assume the one for Kanji is different as well. And taking into account the differences in pronunciation in different languages using the Latin alphabet, I'd say pick one that conforms most to your native language or favorite second language if there isn't an appropriate transliteration for your native language. I once started learning Thai using an English course and that was less than a perfect fit, although my English is good enough to fool most people into thinking I am a native speaker (I am Dutch born and bred).