You could also say "他不在這兒。" or "他非在此處。" and they're written differently because they're pronounced differently. It stands to reason that if someone has a fourth way of saying the same thing with different words, they might also want to write it differently.
Australian say "G'day" rather than "Hello", does the difference of greeting makes Australian-English a standalone language?
Besides, you didn't refute his main idea: phonetic symbol is not equivalent to formal writing.
Australian English and American English and British English are mutually intelligible.
You might as well be claiming that Old English and modern English are the same language.