A bit late to the party, but here is some more information:
1. & 3. yes, the geometry property is `null` because the geometry of a SceneLayer is, like Thomas said, in a binary format. The closest you can get to a readable geometry format is to get its extent, which is a geometry extent: Extent | API Reference | ArcGIS API for JavaScript 4.5. You can then calculate the center point to place the popup.
How did you publish the service? Sometimes popup info comes with the service, so you get the popup with all the attributes for free, and you don't need to configure anything. For example here. What is your use case? Do you want to trigger showing a popup by other action than clicking on the building?
2. Getting attributes: the SceneLayer only downloads the objectId and the attributes that it needs for the renderer. If the SceneLayer has a linked FeatureLayer the SceneLayerView query will query the FeatureLayer for attributes directly. If it doesn't have a linked FeatureLayer then the SceneLayerView query will still make a request to the server, but this time to get the attributes stored in the cache of the Scene Service. I know this is a bit confusing as the queries on the LayerView should be client-side. We are working on a guide topic that hopefully will make these workflows more clear. They are different from the FeatureLayerView.
And about updating the renderer, yes, unfortunately that can't be done using standard solutions, thanks Thomas for providing that hack...
