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In the vast majority of cases, elements with the same SymbolGeometryId will have identical vertices. For example, all these columns will map to the same data as shown:
However, there are some elements that have the same SymbolGeometryId but differing vertices. For example, these highlighted columns in Snowdon:
See the first four vertices of the two leftmost columns:
So far, only Columns seem to match this case. At present, the issue seems to be exclusively translation. These instances could possibly be recovered by investigating each element's transform, normalizing centroids to (0,0,0), etc. If the transforms are removed from the vertices, they could be marked for instancing.