Actually, "Intersect Underlying" is fixed with the latest version. Combined with slope and altitude constraints, this should give you what you need.
It's sorta tricky to exactly configure the feature for your specific terrain, (because Matt has yet to reveal how it really works), but you can get it done with a little try & error.
My take on it's functionality is, that it identifies either depressions or raises on the terrain.
The intersect zone defines how large the area is to take into account for identifying e.g. a depression. (you can define the room between your little fake stones as depressions, or use larger depressions such as found with mountain erosion.
Then, Intersect Shift shall let you define if the areas identified shall be lifted up or down by the specified amount.
I "guess" that minimum intersection shift is similair to an offset for the Intersection Shift.
Good luck,
Frank