Little Navmap is a free flight planner, navigation tool, moving map, airport search and airport information system for Flight Simulator X, Microsoft Flight Simulator 2020, Prepar3D and X-Plane.
At best I can give step climbs and descents which is mentioned here: #295
Setting arbitrary altitude for waypoints is a huge effort and very unlikely to happen. This needs a lot of validation in the profile.
This would be useful for VFR flights, which might necessitate it to pass below TMAs or forecasted cloud cover.