Hello michaelguest,
I suggest to use the following code sample which defines the viewpoint location and orientation required for the 3D PDF export:
chunk = Metashape.app.document.chunk
view = Metashape.Viewpoint()
view.coo = chunk.transform.matrix.mulp(chunk.region.center)
view.rot = chunk.transform.matrix.rotation() * chunk.region.rot
view.mag = chunk.transform.matrix.scale() * chunk.region.size.norm() / (5 * view.height)
chunk.exportModel(path ="D:/test.pdf", format = Metashape.ModelFormatPDF, viewpoint = view)