You are correct. This highlights an unfortunate difference between exporting a Litchi mission as a CSV file and flying a Litchi mission using the Litchi app.
In your case, you set the height of all waypoints at 40 meters above ground. When flying this mission using the Litchi app, the drone will fly to the heights shown in parenthesis at each waypoint. WP1=40, WP2=48, WP3=53.9, FP4=47.9. However, when exporting this same mission as a CSV file, the above-ground heights are written to the file. WP1=40, WP2=40, WP3=40, etc. If this CSV file is converted to an M3 mission, it uses the values in the CSV file which are all 40 meters.
This is an unfortunate result of only storing the above-ground heights in the CSV file. I wish we were given a choice. There is a work-around. Depending on the number of waypoints, this may be time-consuming.
In Litchi’s Mission Hub, create your mission as you have already done with the “Above Ground” option checked. Then, at each waypoint, enter the height shown in parenthesis and uncheck the “Above Ground” option. Do this for every waypoint. This way, the above-ground heights will be written to the CSV file and those same above-ground heights can be converted to an M3 mission.