As far as I can tell from the article and a scan through some of the Atlas (yes, mainly the pictures) the various types and features are all identified by appearance - it feels rather like nineteenth-century biology. I have a feeling that a lot of the "new" features have been included on the basis of "well, we're seeing this quite often, we ought to have a name for it".
I think the basic physics is well-understood, but much of the detail is probably not: atmospheric physics is all about the fluid dynamics and thermodynamics of non-equilibrium systems, in regimes where exact solutions are not possible and you have to work with numerical models and simulations.