I haven't found native ways to read/write higher level metadata.

However, you can use the arcpy Metadata module in a PythonCaller to get higher level metadata, see this link: https://pro.arcgis.com/en/pro-app/latest/arcpy/metadata/metadata-class.htm

import fme
import fmeobjects
import arcpy

from arcpy import metadata as md

gdb_path = r'U:\Joep\fme_forum.gdb'
gdb_md = md.Metadata(gdb_path)

#you can add "\feature_dataset_name" to your gdb path if you need feature dataset metadata
#>>> gdb_path = r'U:\Joep\fme_forum.gdb\dataset_a"

class FeatureProcessor(object):
    def __init__(self):
        pass
    def input(self, feature):
        pass
    def close(self):
        metadata_feature = fmeobjects.FMEFeature()
        metadata_feature.setAttribute('metadata_xml',gdb_md.xml)

        self.pyoutput(metadata_feature)

I have not used arcpy to write the metadata, so no code example for this, but this is explained in the documentation above.

import fme
import fmeobjects
import arcpy

from arcpy import metadata as md

gdb_path = r'U:\Joep\fme_forum.gdb'
gdb_md = md.Metadata(gdb_path)

#you can add "\feature_dataset_name" to your gdb path if you need feature dataset metadata
#>>> gdb_path = r'U:\Joep\fme_forum.gdb\dataset_a"

class FeatureProcessor(object):
    def __init__(self):
        pass
    def input(self, feature):
        pass
    def close(self):
        metadata_feature = fmeobjects.FMEFeature()
        metadata_feature.setAttribute('metadata_xml',gdb_md.xml)

        self.pyoutput(metadata_feature)

Thanks for your suggestion, I used a regular Python script for setting the metadata for the gdb and the datasets, since it is only high level meta. For the classes I still use the XMLUpdater. It’s a bit cumbersome, but works good for now. At least I don’t have to set the meta by hand :)

I made it work by using the PythonCaller as you suggested, thanks for pointing me in that direction. Now I have everything (meta for gdb, dataset and classes) in one workbench.

Very cool!  Glad to be of help