Hello Dieter,
i guess that the geoid file is private so sharing it would be a problem, no?
I would check the metadata of the Geoid Model you have created in Metashape geoids folder. As in following metadata extracted from Geobasis NRW undulationsmodell:
FILENAME=C:\Users\paul.pelletier\AppData\Local\Agisoft\Metashape Pro\geoids\Undulationsmodell_GeobasisNRW_v01.tif
DESCRIPTION=<Undulationsmodell_GeobasisNRW_v01.tif> VERT_DATUM["Geobasis NRW",2005]
...
PROJ_DESC=Geographic (Latitude/Longitude) / ETRS89 / arc degrees
PROJ_DATUM=ETRS89
PROJ_UNITS=arc degrees
EPSG_CODE=EPSG:4258
COVERED AREA=6491497 ha
LOAD TIME=40.13 s
GDAL_NO_DATA_VALUE=-3.40282e+38
NUM COLUMNS=13126
NUM ROWS=8186
NUM BANDS=1
PIXEL WIDTH=0.00028 arc degrees
PIXEL HEIGHT=0.00028 arc degrees
MIN ELEVATION=42.448 meters
MAX ELEVATION=48.483 meters
ELEVATION UNITS=meters
BIT DEPTH=32
SAMPLE TYPE=32-bit Floating Point
TIFF_DESC=VERT_DATUM["Geobasis NRW",2005]
GEOG_CITATION=ETRS89
PHOTOMETRIC=Greyscale (Min is Black)
BIT_DEPTH=32
SAMPLE_FORMAT=Floating Point
TILE_WIDTH=256
TILE_HEIGHT=256
COMPRESSION=LZW
PIXEL_SCALE=( 0.00028, 0.00028, 1 )
TIEPOINTS=( 0.00, 0.00, 0.00 ) --> ( 5.8312400024, 52.5709999995, 0.0000000000 )
MODEL_TYPE=Geographic lat-long system
RASTER_TYPE=Pixel is Area
VERT_DATUM=None Specified
to check that datum is ETRS89 and that all your project.s crs are referred to same datum. And description should be VERT_DATUM=["<Name of datum>",...
where <Name of datum> should be same as datum name you entered in Edit Vertical Coordinate System window during creation of your customized compound reference system....as in following
hope this makes some sense,