I investigated this a bit further: It’s not only harmonics, but it seems that the transpose -function in general does not work if a playback technique with articulation type “direction” is triggered.
Steps to reproduce:
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in your expression map (for any library), assign arbitary transposition value to for example pizzicato -technique
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in the score, place any playing technique with articulation type “direction” before it. It may be listed as an add-on technique in the expression map, but that doesn’t actually matter.
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Pizzicatos are not transposed anymore (but are still triggered)
I hope I’m right with this, since I don’t want to waste your time… 
But this seems how it behaves on my computer.