lacks accuracy of chord, extensions, alterations, and inversions
Assuming equal temperament, can you not eliminate overtones that are not octaves of the fundamental by identifying the comma? Then you are left with fundamentals and their octave overtones. You would have all extension and alteration notes; separate out transient lead notes (but still show); from there an algorithm could be used to determine an accurate inversion(s); this may produce something different but something very good; e.g. if the guitar is paying D7 but the piano is hitting E and B notes, you come up with a D13 on guitar.