Same here. If I fly a mission where there is limited turning there is no issue. For me it only happens if the speed gets high enough to where the heli "cuts off" waypoints (due to speed and acceleration limits) and continuous turning on the mission. I think I have enough data on it to be able to submit a proper issue on GitHub so the EKF experts can take a look at it. I'm thinking some kind of error or "leak" in the code that causes a gradual buildup of the error with a resulting decay of the altitude estimate. I think it's showing the desired altitude at the final waypoint as being way low because the error gradually "leaked" to where it thought the sensors drifted that far, resulting in the altitude estimate also drifting.
I eliminated hardware issues by reverting to 3.3.3 and flying the same mission with no issues. And it is repeatable on the mission illustrated above, although the drift in altitude is not always the same amount.
When I looked at your issue before @pmshop I was convinced it had to be something else. Because the logs don't really show what's going on or indicate any error. Everything looks rosy - right up to the point where the aircraft flies into the ground. The ground station indicates proper altitude, and everything, during the flight. If I went back and looked over your logs now, with what I have learned by analyzing mine, I'm betting I'd see the same anomaly. It was much harder to pick out on your flights because it was over changing terrain elevation. My documented "problem flight" is on perfectly flat terrain where the decay in the actual altitude can be easier seen thru the baro readings, visual reference, and onboard camera reference..