system-config-display-1.0.37-2 does disregard the local keyboard setting and configures a new xorg.conf file with the language "us". Subsequently calling system-config-keyboard and confirming the german latin1-nodeadkeys option fixes the file.
Turns out that system-config-keyboard is just as bad. If I change the layout there, it messes up the configuration of the running X server and confuses the keyboard indicator applet to the point where it cannot switch layouts anymore.
I did call system-config-keyboard in text-mode. So there was nothing on the running server to mess up.
*** This bug has been marked as a duplicate of 145316 ***