As you intuit, there is no reason to presume that Navier-Stokes would be unreliable at macro scales relevant to meteorology, simply because it is so thoroughly tested in experimental settings and to such sensitivities that it is known that all relevant factors are accounted for.

(Of course, why would one presume that if it is inaccurate at planetary scales, it biases observations towards the climate change narrative? It's just the typical “God of the gaps” kind argument.)