(This is for my own understanding.) SHiELD and AM5 have different atmos_drivers/*/atmos_model.F90 as the interfaces to the AM5 and SHiELD physics are different, especially with respect to radiation and surface coupling. They also have different GFDL_atmos_cubed_sphere/drivers/*/atmosphere.F90 as FV3 needs to prepare inputs for the physics differently (AM5 takes 3D arrays, SHiELD physics takes 2D blocked arrays).
This does suggest that as we move towards unifying the two atmospheres, we would need to reconcile their interfaces and data structures. It is something to keep in mind going forward.
@bensonr @JosephMouallem