Yes, I can do this by changing the projection of the shapefile before transforming it to CityGML. Based on this reply, the Cesium World Terrain coordinate reference system (this is the terrain I am trying to clamp to) is EPSG:4979. But I can’t reproject the shapefiles into that coordinate system because EPSG:4979 is a 3D coordinate system and shapefiles are 2D. What is otherwise a good coordinate system to begin with?