What is the z-level stuff? Haven't you always been able to move through layers up/down?
Underground river -> Chasms -> Magma -> Bad Things(tm)
The real trouble I had with the old versions was the inability to build walls. As I recall, once you dug something out it was dug forever.
I don't know the minimum off hand but it is probably around 6 normal stone or cave levels, minus the levels used for open sky space and magma sea which I don't know the minimum for. Trees are multilevel now and I don't know that they will grow on a single layer.