The scaling is relative to the hotpoint, so it's really important to place it at the base of the tree. But if this is done, the trees shouldn't be elevated over the ground. They can look elevated in the real time rendering because the terrain use a lighter version of its mesh to be displayed, but the final rendering should be fine. Can you send me your file before the replication is done and the parameters you used if you still have a problem, I'll look at it. And I'll update the tutorial this week end and put the scene and the shader available for download.