Its sounds like you really want a 3D physics engine to be honest.
One thing to keep in mind is that both Chipmunk and Box2D perform the collision detection in 2D. While layers can let you fake pseudo 3D collisions much like Little Big Planet does, you can't actually smoothly transition between layers. It's either in a particular layer or not, and there is nothing to prevent you from moving into a layer occupied by another shape. You also don't have any shape in the 3rd dimension, just whatever extruded shape it is in 2D.
Lastly, the collision detection is optimized for 2D. Both engines use 2D spatial indexes to speed up the collision detection. This means that when you have a lot of objects that overlap in the xy plane, the collision detection can get pretty slow.