After a call with ESRI support I honestly can't believe this isn't already implemented-
If you set up a Configurable Web app using a 3D scene, you can select a template with an inset map that links to another 2D web map. This is great, and looks really good. The issue is, you cannot toggle layers so whatever is the top most layer in your scene and web map are the only things displayed.
If you use Web app builder you can add the layer list widget without any issue to toggle layers in your scene. You cannot however add a 2D map inset.
The functionality is all there, you can have an inset on a 3D scene and you can toggle layers on a 3D scene, you just can't do it together without creating a custom widget yourself. Is this not a major oversight? The ability to turn layers on and off is one of the things most central to making these web apps useful