These are some of the main differences between 2 given numerical weather model.
With that being said, the same model will give different results when run on a different computer (Hong et al. 2013).
Hong S-Y, Koo M-S, Jang J, et al. (2013) An Evaluation of the Software System Dependency of a Global Atmospheric Model. Mon Weather Rev 141:4165–4172. doi: 10.1175/MWR-D-12-00352.1