Hello jvduijvenbode,
Are you working with the stand-alone Metashape Python module or via program GUI / from command line with "-r" argument?
In the latter cases, if you already have the geoid file in the /Metashape Pro/geoids/ folder, then there's no need to register the geoid again. This method "addGeoid" is mostly used for the stand-alone module to define the paths to the geoids to be used - it wouldn't modify the existing system.
If you want to use the system with the height above the geoid, you should either define the coordinate system by existing EPSG code, or provide WKT definition of the system.