Robert,
Thanks again for the attempt to clarify. Maybe I am missing something here.
If I have two FeatureLayers I can control which FeatureLayer is displayed on top, just as if I had two Graphics Layers. So essentially since all my layers are treated as individual FeatureLayers in WAB instead of a Dynamic Service, I should be able to control the order.
I get what you are saying that FeatureLayers/GraphicLayers are drawn above all else, but the order of those can be controlled if there are more than one of those at the top. So if I added 2 graphicsLayers to a map, the one added last would be at the very top.
If I am not understanding this correctly in reference to WAB would you elaborate?
Cheers