Hmm, I suppose one way you could get around the issue is by using two Viewport nodes. I've done it before, for this tutorial, but I didn't really go over the topic of setting up the Viewport nodes because it is kinda confusing and fiddly, and I didn't want to add extra complexity to what was already going to be a somewhat complicated tutorial subject.
I don't remember exactly what I did to make the two Viewport nodes work, but perhaps downloading and poking around the project you'll be able to find out. I do remember that getting physics to work on both Viewport nodes was interesting and took a lot of trial and error. I also remember that keeping the camera's in sync required writing some GDScript, as the RemoteTransform node had issues.
Other than that, I'm not sure.
I'm not too experienced with shaders, but it is also possible that you could write a shader that performs similarly to the UIOverlay shader in Unity. If you want to go the shader route, I would look and see if you can find a GLSL shader that works like the UIOverlay shader, and then see if you can port the GLSL code to Godot's Shader code.
Hopefully this helps!
