I have a scene created with various datasets: hillshade, elevation layer, 2D/ 3D features, multipatch, ortho and etc. After bringing it into data in Experience Builder, I got an error and could not use it in the map element. Since it is a scene, I assumed that it's on JSAPI 4.X, and not sure why there is an error (see my reference below). Is ther e any layer types that are not supported by Experience builder yet? I was able to bring another scene successful thought that has only hillshade and orthos.
Select data—ArcGIS Experience Builder | Documentation
Web maps and web scenes created with JSAPI 3.x that cannot be opened in Map Viewer or Scene Viewer cannot be used as data sources. (If you add one of these items, it won’t be available to select and appears in the Data panel as an error card.)