Yesterday I updated TW to the latest release.
I did not update for a few weeks so unfortunately I cannot tell which snapshot would have triggered the issue first.

The problem was that uid, gid and directory permissions did not match any longer and I can tell that I never touched them manually.

In older versions of my passwd polkit was using 
uid 472
gid 472
which at some point switched to
479:479

/etc/group still had polkitd=472 and the rules.d directories were only readable for root and group polkitd.

Since user polkit now was assigned 479 it could not access the rules anymore which made the service start fail which on the other hand created a horrible mess when starting up the desktop.

I think I fixed it now by changing "everything" to 479 but I'm still very curious why updates created that mess.

As a sidenote it seems chrony was gid 479 before but now is 463 in passwd but still was 479 in group. So also had to change the chrony assignments and file permissions manually. There is a chance that some things are still messed up though.