Hi Marc,
We have noticed that sometimes with the Mavic 2 Pro there are some calibration issues if the default parameters are used. We instead recommend using the All prior option for the Internal Camera parameters optimization, if the camera optimization does not give good results.
Could you share with us the quality report of the project?
You can follow this post of our Community on Mavic 2 Pro issues and particularly read this comment by Daniel.
Also, the Error estimation in volume calculation is strictly linked to the GSD of the project and the bigger the area is, the bigger the error will be. You haven’t mentioned any GCPs. Are you using some to increase the Accuracy of Pix4D outputs?
Relatively to the vertices picking, you can have a look at this other post of the Community. Is this what you were looking for? I will consider adding the suggestion you pointed out in point 5 of your list.
Finally, concerning the data acquired with the Topcon/Magnet system, you should first convert the coordinates to the output coordinate system in Pix4D or if you want to work in your local system, Pix4D can compute the transformation parameters to your local system with the site calibration functionality. I would say that would be the best option.
Cheers