I don't understand the problem...
What kind of vegetation? A surface layer, or an object population?
The negative values are normal, because the planet surface (y=0) is displaced upward and downward (white (y=+100) and black (y=-100) of the powerfractal). This happens all the time. As long as the population is set to follow the terrain of the compute terrain (and you don't have any other displacements after that), it should follow both hills and valleys. I downloaded your file and I created a population of rock objects without any problem.
below is a little test render to show that the population does appear correctly. I disabled the atmospheres and clouds for render speed, and it is a crop-render...