SceneLayer with associated FeatureLayer (SLwFL) from Multipatch FeatureClass on FileGeodatabase is the only way to go (or at least the most flexible) for building interactive apps because they offer more functionality than simple standalone SceneLayers.
Current state of things (ArcGIS Pro 2.9):
-> Automating the Creation of SLwFL from filegeodatabase multipatch Feature Class: workflow not documented, the most resembling solution is what i posted in here and it does not work well because of layer settings https://community.esri.com/t5/python-questions/can-arcpy-publish-update-web-scene-layer-with/m-p/448...
-> Automation of Overwrite SLwFL already available in AGOL/Enterprise, it simply is not documented and currently the idea is to "republish" although it would create a whole different ItemId, it should be like this for Overwriting FeatureLayers https://community.esri.com/t5/arcgis-online-documents/overwrite-arcgis-online-feature-service-using/...
So if you have a large scale 3D model to deploy, and which is dynamically changing? Current solution is either: do it manually with the ArcGIS Pro GUI which is not viable for multiple models or try your luck using the script i posted in the first link. Regarding overwrites or updates, automation simply is not possible (have to rebuild whole feature class again).
In the use example here have made a way to make it work, although these features are such a basic and important set of tools, reason feedbacking over here in.
If someone of dev ESRI reads this would be welcome in advance if could add something.
cheers
