I wonder what would be a workable user interface for such multi material switcher. Would for example having a single sphere in the scene per a single set of materials work well for you? For example, if you have three configuration options for a kitchen, you would add three spheres in the scenes, somewhere in the kitchen. When the user clicks the first sphere, the first set of materials is applied, the second applies the second, and so on.
By the way, having overleaping geometry is not necessary if you use the isolated shadow function, that allows to disable shadow castings for some objects.