There is no technical issue. It's just the way the autopilot does it. It takes off and climbs at whatever you have your vertical speed set to for WPNAV. It's not smooth like a human pilot. If you have your WPNAV's tuned up for high-performance flight, it's downright scary with a big heli with a lot of power. It's a rocket and if you have your WPNAV_ACCEL set to 980 it will accelerate at 1G with the throtlle wide open and the collective maxed right out. So have to use values around 500-600.
I prefer to take off smooth with me flying, do all my checks, line it up, use a spline curve into the first waypoint to control acceleration, and use the Channel 6 tuning to dial up the WPNAV_SPEED a bit at a time to mission speed. I use the same procedure in reverse on approach - disengage the autopilot before it gets to the final waypoint and take over manually. Because can't let the autopilot bring it to a stop by itself either. It's way too dangerous.
If you set the WPNAV_ACCEL down so the autopilot isn't as rough with it, then it won't hit waypoints at 27 m/s.
The autopilot is basically like a student pilot - let it fly the heli, but don't let it do anything that requires precision
The issue is the nav controller. It was never designed for high-performance aircraft. With enough experience you learn how to fly the system, how to flight plan for it, and how to work around it.
You will see the issue there is the huge pressure buildup under a 6 foot main with a heavy heli, causing the altitude estimate to vary (I've seen it at 5-6 meters before in no wind). As soon as you shut the heli down the altitude goes from negative relative value to normal. The bigger and heavier the heli, the worse it is with a barometric altimeter.