So the good news is, that I was finally able to remove the layer shift in the benchy with test print #15.
The bad news is, that it was sliced with Slic3r...
But this finally proves, that this is a Cura problem, and hardware problems can be excluded from the list. And as I tested so many different parameter settings, I would finally say the chance that this is a bug is very high.
I also noticed, that all other but 2 minor line problems (including 2 other shift locations) are gone in the #15 print. As it was my first print with Slic3r at all, and I did only transfer the Cura profile to Slic3r, the overall print quality is ok but worse than the benchies made with the calibrated Cura.
So is there a way to do a bug report about this?