Sorry for the delay. We feel that Nemeth symbols should be used, and that the spacing should follow print. I can see how there are times the transcription will be ambiguous. Those cases may benefit from a transcriber's note explaining. Are you disregarding the capitals? If so, the commas will be unlikely to be misread.
Please send examples of formulae that you find to be difficult. It would be interesting to see how they look in braille.