I am a little confused. At the beginning you talk about PSD/PDF and now about PSD/JPEG.
Unfortunately, I can't see where in your PSD the threshold is applied. But since you are most likely overlaying a smart object above with reduced opacity and possibly with a blend mode, please try the following: Before saving/exporting your file as a JPEG, activate the top layer and press Shift+Ctrl+Alt+E. (This will create a merged copy of all visible layers above the active layer).
Does the appearance of the file change? If not, then save this version as a JPEG.
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