FYI: I managed to fix this in PyVista. See https://github.com/pyvista/pyvista/pull/799
In summary: vtkSelectionNode was giving us the cell IDs after running a vtkDataSetSurfaceFilter and a vtkTriangleFilter (figured this out by guessing). So we have to mimic that pipeline to map the selected cells in the selection node back to the original mesh.
An important note… the representation style MUST be surface!!! Using wireframe or points styles on the property will break this pipeline.