First off; Toposurfaces are SURFACES only - not solid geometry. The solid representation you see when the Toposurface is cut is smoke and mirrors. Now, regarding cutting a "hole" in the Toposurface: I wouldn't. But if you must, then use Split Surface to sketch the hole and then delete the Split Surface. Again, I wouldn't. It's silly. But whatever.
...have you thought about using a deep Building Pad? Try it; you'll like it.
