Yes, I have replicated the problem with your data. This in on my AMD 48 thread desktop:
~/Develop/Voronoi/build/bin/vtkpython GeometryFilter.py
Time to vtkDataSetSurfaceFilter: 6.067303895950317
Num output points: 64161
Num output cells: 128450
Time to vtkGeometryFilter: 0.09132719039916992
Num output points: 64161
Num output cells: 128450
Even when I set the maximum number of threads to 1, there is an appreciable difference, although notice that vtkDataSetSurfaceFilter is running in about the same time (so it looks like threading is not functioning). Is it possible that you are running a modified/older version of vtkDataSetSurfaceFilter? I’ll check with Spiros and see what he thinks, I feel I am missing something obvious 
~/Develop/Voronoi/build/bin/vtkpython GeometryFilter.py
Time to vtkDataSetSurfaceFilter: 5.950025796890259
Num output points: 64161
Num output cells: 128450
Time to vtkGeometryFilter: 1.6691839694976807
Num output points: 64161
Num output cells: 128450