Auto Mission Altitude

I'm trying to get my copter to use input from a rangefinder rather than the barometer during auto missions. I have a lidar-light with a max range of 40m and am flying at 10m. The lidar provides alt measurements via the sonar-range status and these roughly agree with the baro. This is until I meet some terrain. The Baro doesn't see small changes in terrain causing the heli to fly at 7m AGL when there are small hills. the lidar-light measures these altitude changes perfectly. The problem is that I can't seem to get the system to use that data in any situation other than landing in loiter (and even then I'm not sure if it is using it). 

My system is a pixhawk running 3.2

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