Managed to fix it, but it was quite a “journey.”
- Safe boot did not fix it.
- Onyx is not yet available and would likely not have fixed the problem.
- Logging into another account did not show the issue.
- Changing the Home folder of my account to first a restored and then an empty one did not fix the issue. This meant it was not governed by anything in the $HOME folder hierarchy.
The solution was to create a new account and then assign the my main home folder fixing the ownership. Doing this via commandline makes it fairly quick. When that looked good I deleted the original account and change the name and User ID fo the new account back to my original one (501).
I always have my home account as 501, because it makes it easy to access home folders across multi boots or mounted disks.
Various security settings had to be reentered, but all was well.
I am not sure what the macOS system user database is called these days, since the days of /etc/passwd are long gone.