I'm confused about setting the Scene's coordinate system vs the source data. Looking for a way to 'burn' proper Z values into the models so the are always at the default Esri terrain in WGS84.
If you have 3D Object Multipatchs which have absolute elevation based on the coordinate system they were generated. They will float to that elevation when published as a scene layer.
In Pro when a 3D Object Multipatch layer is loaded it is placed on ground in the scene. If you open the Layer properties and navigate to Elevation insure that the features are "At an absolute height". This will place the feature at its correct elevation. if the data is floating over the terrain open the layer properties once again and adjust the "Features are" properties to "on the ground". You will now see that the feature conforms to the WGS84 World Elevation Service that is the terrain in Pro.
Now you will need to "bake" this elevation into the feature. This can be done using the "Layer 3D to Feature Class" Geoprocessing tool. Once you have processed your data you should be able to output a scene layer package which conforms to the WGS84 Terrain in ArcGIS Online scene viewer.
For further information please check the white paper on "Publishing Hosted 3D Feature Layers" or review the ArcGIS Pro tutorial "Author and share local scenes to Portal for ArcGIS"
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