Dear Abhinav,
Regarding BeamDyn, “yes”, the version located at wind.nrel.gov/public/jjonkman/BModes/ is the newest version. See the following forum topic for an explanation of the differences between the two versions: Run BModes with Hydrodynamic effect..
There are several versions of the tower for the NREL 5-MW turbine, depending on the substructure type (monopile, tripod, jacket, floating platforms), but in most cases the diameter and thickness vary uniformly along the tower length.
Best regards,