You are talking of a very neat features that some solid modelers have (Solid Edge, Spaceclaim). Rhino is surface modeler for the most part as I know.
I think that what you want is closely related to the very specific algorythms solid modelers use to represent ‘topology’ (one of my favorites subject). Basically there are three states of a point compared to the solid object: in, on, out (‘on’ is like ‘in’ the boundary surface, a part of the surface).
I think Rhino has a concept of a frontface (normal vector=1) and backface (-1) for its created surfaces. Maybe those “binary” states are the key to better solid representation, fliping normals accordingly when boolean operations is applied, etc…
I am also thinking of something like: defining a surface as a ‘ClippingSurface’ with the respect of its boundaries (not as an infinite plane or whatever). Just analogy I make here.