OK, I think i found a solution for my issue.
Basically I did it like described here Docker Restarting: KARAF_ETC is not valid: /openhab/userdata/etc but that still ended up in the above issue.
I then realized that I may have started the container initially without the user/group of the NAS but I thought since I’m shutting down the container it will recreate everything internally. As to my knowledge this is the default behavior of docker containers (to not store data internally).
It seems the Synology docker app is still keeping this.
So I had to select the container in the Docker app and click action > reset (hope it is called this way in English as well as I have it set to German where it is Aktion > Zurücksetzen).
This really cleans the complete container and after restart I see that the user & group are now taken over.