@drrabazz
This article about ECMWF model may give you the information you are looking for on the orography model that is integrated into the weather model itself. Indeed the orography model corresponds to a coarse and simplified terrain profile.
All weather models use such a terrain model, which is generally more precise in high resolution weather models.
Then there is the effect of the horizontal resolution (9km), on the uncertainty. Here is an example in the Swiss Alps. The cloud base is at 0m in the purple square i.e. both above the Matterhorn at 4400m and above Zermatt at 1500m ! The square dimension corresponds to the model grid spacing.
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