How To Prepare a Digital Terrain Model for Terrain Awareness Mode with Phantom 4 RTK 

When I downloaded the data it was already in the Slovenian coordinate system, I just had to change the orthometric elevations that the terain model was in to ellipsoidal heights that the drone expects.

The x and y coordinates of the starting point can be anywhere, meaning at the location of your take off. Since you defined the terrain elevation and the desired AGL, the drone will simply lift up to that altitude and start the mission.

You could also manually fly the drone to the start point if it's over 400ft AGL from your takeoff point, visually following the terrain to technically keep it under 400ft. You can then start the mission while the drone is already in flight. I always start my missions by manually flying to the start height to confirm camera settings at that height anyways. I had this issue with a cinema flight from a monument on the top of a mountain. I was 20ft AGL at the monument, but when I flew 100ft away from the monument over the cliff, I was 1000' AGL. In Canada we are allowed 200ft horizontally from a building or structure, but the rules don't actually cover steep terrain or mountains with a sharp cliff or drop off, since a mountain is not a structure. 901.25 (1) Subject to subsection (2), no pilot shall operate a remotely piloted aircraft at an altitude greater than (a) 400 feet (122 m) AGL; or (b) 100 feet (30 m) above any building or structure, if the aircraft is being operated at a distance of less than 200 feet (61 m), measured horizontally, from the building or structure.