There's a tool in the lot editor part where you can cut a hole on the ground in a cell area (the hole will always cover one cell and cannot be cut halfway between two cells i.e. half of the cut is in one cell's area and the other half is on the other cell's area - however multiple cuts will combine into a large cut if they are in adjacent cells). This allows "underground" structures such as cellar doors that are a bit lower than 0.0 to be possible but it requires a lot of planning when modeling to get the underground parts in the correct location. It is also a similar way we created the metro entrance where the escalators go below ground. But it's not exactly the same as what you are describing even though it is in a way similar.
I made a mockup on 3DS Max of how the cutouts will appear when done on a 4x4 cells lot:
Mockup of the lot cutouts.