you must change all the altitude constrains to height for the arrival and departure and missed approach, so that if any turn is based on altitude the fms will handle it correctly.
approach, from faf to threshold are prohibited and non-sense, as the fms calculates the approach path to 50ft to the threshold based on qnh.
most of the times you will get an msg to check fpl altitude as in the fms logic you are going to fly below the airport altitude.