To clarify, the height of way points is based on AGL (altitude above ground level). AGL is set by your starting point/home point, which is 0m on the ground. If you have a natural change in elevation over the course of your mission, it is not accounted for when setting subsequent waypoints. Say you set one far away at 100 ft high, but the change between the elevation between your home point in there is 50 ft, then your phantom will only be 50 ft from the ground.