Hi Nazanin
Re 1) Yes, you can do that, though you need to double check for bad flips and very likely need to flip a few cases manually via ParaToSPHARMMeshCLP. Use ShapePopulationViewer with the phi and theta coloring to check for flips. Use it also to check for appropriate correspondence without the additional parameter space alignment). 

You though still need the procrustes alignment, as the pre-alignment is usually not good enough and you don't want any translational and rotational effects in your shape analysis.

Re 2) No, we did not use landmarking, but rather the approach that you are suggesting in (1). If I remember correctly, we added that option specifically for that paper. It's less optional compared to the landmark solution, but appropriate.

Martin