I am not working with such repertoire, but it might be interesting to explore the possibility of annotating polytonal lines or superimposed chords in works that are still tonal, or which have a strong tonal base. Would it be reasonale to add:
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two harmonic labels to a single note, vertically aligned on the score, for polytonal passages?
(These is just an invented example: no real annotations)

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a new symbol (for instance * between two harmonies that are superimposed? eg. I6*IV7