Use cut and (new) edge fades to white

[Ofnuts]

Think the culprit is here:

Code:

   pdb.gimp_image_select_polygon(image01, CHANNEL_OP_ADD, len(polygonPoints), polygonPoints)          #temp add this back
   pdb.gimp_selection_invert(image01)
   #~~~~~~~~~~
   layerobj = layerdata[i].layerobj        #-()
   pdb.gimp_edit_cut(layerobj)
   pdb.gimp_selection_invert(image01)

   #---  darken all but the top layer  -----------------------------
   if i != len(layerdata)-1:
     pdb.gimp_hue_saturation(layerobj, ALL_HUES, 0, layerdata[i].lumsadjust, layerdata[i].satadjust)

The polygon selections create partially selected pixels. This is normal. When you cut, these partially selected pixels become partially transparent and you get a smooth cut. However, you keep that selection. So when you apply the hue-saturation, the effect of the hue-saturation on these partially selected pixels isn't as strong as on the other (fully selected) pixels and since the goal of the hue-saturation operation is to darken things, these pixels remain lighter.

The fix would be to remove the selection before you apply the hue-saturation... AFAIK H/S only applies to the RGB channels and will leave the alpha channel unchanged.

Edit: another possible fix is to to the Hue-Saturation change before the cut...