Pdf export has some difference in comparison with drawing in Layout, specialy transparence or 3D view use X Ray.

Export of shaded (rendered) views, which can be only exported using rendering GsDevice. The result in this mode can be different depending on using device, which should be created on Applictaion services side, not by PdfExport itself.

You can try to use GLES2 device for export such views - this device has the best functionality to draw non-simple geometry objects.