Simply put, VCarve does the math for you when it comes to setting Z zero.
When you set it to the top of the material all Z cuts that are into the material will be a negative value (below zero)
If you set it to the spoilboard all Z cuts will have a positive value (above the Z zero).
Back in the day, like a hundred years ago, the standard practice when milling on an expensive vertical mill was to place the Z zero at the table surface. That way any Z value that was negative stood out indicating the machine was about to get its bed milled or drilled.
Low Profile CNC Router Vise