Using Phantom 4 Pro. Whenever I run a 3D Mapping task with GSP Pro 2. The task completes normally and photo are successful. When I look at the altitude information in the images they are all correct relative to one another but woefully inaccurate for actual height.
To test this I ran a task where I knew the altitude exactly, (29.7m). My first run produced altitudes of around 67.13m with an altitude reference of "above sea level". The height flown was 20m above take off height.
For the 2nd test I used drone deploy as the misson controller. I was pleased to see the altitudes in the new set of images where correct!. It doesn't say too much for the manufacturers software (DJI)
The images from both missions where processed using WebODM. The output from these missions produced the same orthos and the same DEM files. Contours where very similar and close. the Point cloud produces a similar 3D image with the drone deploy's 3D slightly better. Probably because the collection process is the same. They both used the same equipment. Phantom 4 Pro  (no firmware changes), iPad Mini latest, iPhone X, iPad pro with IOS 13-15.
Its obvious, something in the capture process instructs the DJI Phantom 4 Pro what to put in the images files for altitude. Will Ground Control Points have any effect on this. They would be a very expensive solution to what looks like a bug.

It's not a bug
http://www.ga.gov.au/scientific- ... /ahdgm/ausgeoid2020

LV_Forestry Posted at 2-20 07:58
It's not a bug
http://www.ga.gov.au/scientific-topics/positioning-navigation/geodesy/ahdgm/ausgeoid2020

Thanks for your input. A lot of reading and concentration required for that subject.
Incidently the location where the activity took place shows an altitude difference of about 100mm when converted to ausgeoid2020.

What it doesn't do is show the massive differences in the altitude stored between dji ground station pro (way out of wack) and drone deploy very close to actual.

I have just deleted and re-installed ground station pro 2. I ran a new 3D mapping profile a couple of days ago using it and suddenly its with a couple of meters. I am beginning to think the problem may be related to the Phantom pro firmware. Instead of just waiting for the drone to report the gps is ready, I wasted another couple of minutes with GPS lock before starting the mission. Maybe the problem is related this. Who knows.

I think your expectations are much higher than the precision that a P4pro can provide.
Up to 5m error without using RTK is not shocking. There are plenty of solutions to fix this.