It is my understanding that the large scale fluid flows are more or less the direct consequence of fluid motions on a rotating sphere, given the constraints represented by, for the oceans, the land-ocean interface. The topology of the surface of the solids is not resolved by the models and codes, so if the large scale is correctly calculated, that must not be critical.
On the other hand the states of the atmosphere at regional scales is sometimes determined by the mesoscale topology of Earth’s solid surfaces; monsoons, rain shadows, &etc.
It is a given that calculation of the weather, the perturbations in the state of the atmosphere at a given location caused by distributions of energy input and redistribution of the prior content, is beyond reach at the present time.
Further, for decision support only the weather that counts. (And possible changes in the volume occupied by Earth’s oceans.)
The task then is to determine, at mesoscale, the changes in the weather due to changes in the composition of the atmosphere. I think this is an impossibly tough problem.
Getting global scale-metrics roughly right has the same importance as getting the lightening strikes to ground dead on. Interesting, but not very useful.
Climate is what you expect. Because that is determined by where you are on Earth’s surface, the time of the year in Earth’s orbir around the Sun, and a couple of other factors, including in some cases mesoscale topology.
Weather is what you get. And that, “what you get” is what is required to be determined for decision support.
To get a different perspective on calculation of atmospheric flows, use The Google with S. Lovejoy, D. Scherzer and A. F. Tuck, in combinations and separately as author(s), and atmospheric turbulence as keywords.
Clouds are, I think, are described solely by parameterizations; including their vertical motions. Possibly an outcome of the state of the vertical component of the momentum equations.