These settings work for me (in my test project at least :smile: ):
Here is how you do it:
Set the world enviroment background to canvas. Make a Control base node in your scene, not parented to a CanvasLayer, but rather just somewhere in the scene (in my example the Control node is a child of the Spatial that is the scene's root). Place whatever you want as the background in that Control node.
If you want to make GUI that draws on top of the entire scene (like the GUI normally acts), then create a CanvasLayer node and attach whatever you want as your GUI to that (assuming it has a layer value of 1 or greater).