This problem is not limited to Russian, and is in fact much worse for other languages like Thai, where the spelling of words is only loosely related to the pron

This problem is not limited to Russian, and is in fact much worse for other languages like Thai, where the spelling of words is only loosely related to the pronunciation. You can optimize for accuracy (transcription) and lose the phonetics, or you can optimize for phonetics (transliteration) and lose the ability to reconstruct the original script, but you can't do both.