I see @ARFLme! Is there some GLshader (I'm not even sure what shaders can do or cannot do) that can be applied on Scene objects (not the whole scene) and allow the particular scene object to be blended with the underlying layers in a manner other than opacity? eg. multiply blending, additive, substract,divide etc?
Simon is the best one to ask about the shaders. He's the one that implemented it into the source code & wrote the shader toolkit script which is available on the script index page of the wiki.
To my knowledge only some of the premade shader effects can be applied to scene objects though it's possible if you have enough savvy (I don't) to write your own shader functions & effects to apply to the scene / scene objects, etc.
You could actually create an image the size of your scene which contains the background & all of the static objects that can't be manipulated/picked up. Other than that I don't know... I still think best approach would be 2 scenes. Getting the position of all your characters on current scene & teleporting them to same position on the new scene is pretty straightforward.