the difference between projecting data and changing a dataset's spatial reference

Is there a difference between

1) projecting the data in a feature dataset using arc toolbox->data management tools->Projections and Transformations->Batch Project
and
2) changing the spatial reference on a feature dataset

Also, does anyone know a way to reproject data using something other that arc toolbox or the python arcpy.project_management method? Perhaps something in c#.