The SAFE are the data originally disseminated by the European Space Agency. The SAFE format is basically a ZIP file with a collection of XML and other files. Within the SAFE file, the spectral bands are presented in the native spatial resolution of the satellite sensor. On the other hand, in the NetCDF files all bands are interpolated to the spatial resolution of the band with the highest resolution. This provides and image stack that is easy to use in processing. Furthermore, the NetCDF files are also available through OPeNDAP allowing data to be streamed into applications without downloading files.
If the user want data in the native spatial resolution from the NetCDF files, data can be subsampled to the original spatial resolution without information loss since the interpolation used is nearest neighbor.
Another benefit of NetCDF is data can be aggregated in time or space using an application server. This will allow extraction of data from e.g. multiple Sentinel-2 tiles or a time series of one tile. This is however yet not implemented. In the current setup, the NetCDF files lack some of the auxiliary information provided in the SAFE files.