That would be a great functionality indeed come to think of it. Like two mirrors that face one another multiple layers could be shadowed out progressively or incrementally and when clicked on brought to the foreground. Perhaps an infinite number of layers would be pointless but that two or three or more be set up in such a way seems self-evidently practical and efficient for numerous reasons. I'd love to be able to fit so much into an otherwise confined space without at the same time compromising the smooth appeal that the diagram format presents. Lots of diagrams merely introduce that which requires a great deal of language if to be explained completely or thoroughly however in a diagram format so much information simply defeats the purpose of having a diagram. Yet if a third dimension (depth) were introduced it'd make it so that the user could simply hover their cursor over the opaque shape or text and as a result the two layers swap such that the foreground becomes the background and vice versa. It's basically the same principle that the brain makes use of in folding in on itself so many times over: because it is confined to a given space the only way it can grow or be bigger in the same area is by folding in on itself. Here too it'd seem aesthetically consistent and intuitively smart for the viewer. Mere color coding could help the user to distinguish between the multiple layers as could the degree of shadowing of course. 

Hi Justin

Thanks for posting! I hope I'm responding effectively to your questions. What I would recommend is to place a hotspot on a shape and to set the functionality of that hotspot to toggle layers. This would allow you to maintain an additional process that would only appear when clicked (see gif). 

Please let me know if you have additional questions about this!