This can be done in another way:
• Wrap your prefab into new GameObject.
• Move the inner GameObject up.
• Create a new prefab from the outer GameObject.
• Use a new prefab for your 3d markers.

The problem is that the zoom is very small, and you just do not see the altitude.
Increase the zoom and you'll see that the markers are flying.
I made a test script, and it works fine.
If you need, I'll attach this script.

I am having difficulties setting the height of a 3D Marker. We have a map on which a player can walk and it displays objects based on data (for example high object for high danger level). For this we decided to use the 3D Marker because it works with latitude and longitude.

I've tried using either a 3D vector instead of 2D or setting the altitude manually, but they still appear at the origin of the Y axis.
Example:
// Marker position. Geographic coordinates.
            Vector2 markerPosition = new Vector2(Random.Range((float)low_lon, (float)high_lon),
                                                 Random.Range((float)low_lat, (float)high_lat));

            // Create 3D marker
            marker3D = control.AddMarker3D(markerPosition, markerPrefab);
            marker3D.scale = 20;
            marker3D.altitude = 1000;