After talking to the people at Litchi and doing my own testing, I can confirm that this limitation is based on the VPS forcing the Mavic up to 2 meters. This particular limitation has nothing to do with the home point altitude. I've turned off every other protection and it will still get pushed up to 6 feet. But once I turn off VPS the mission will run at the actual height entered into the waypoints. Unfortunately, it flies terribly without VPS so it's pretty much unusable without VPS on. It moves up and down to much. It will eventually crash. And either way, the footage is pretty bad. I'm still looking for a way around it, maybe modifying the firmware, but as of yet, I have no answer.