I have no idea why but Ubuntu doesn't allow to configure the screensavers it comes with. Not those screensavers were not configurable, but in contrast to xscreensaver-demo, Ubuntu itself does not offer access to their visual config :-( What I wanted to do is stop GLMatrix from rotating the matrix, which would have been -no-rotate on the command line. Editing glmatrix.desktop in /usr/share/applications/screensavers finally helped:

The modified file looks like this:

[Desktop Entry]
Encoding=UTF-8
Name=GLMatrix (without rotation)
Comment=Draws 3D dropping characters [..] by Jamie Zawinski.
TryExec=glmatrix
Exec=glmatrix -root -no-rotate
StartupNotify=false
Terminal=false
Type=Application
Categories=Screensaver
X-Ubuntu-Gettext-Domain=xscreensaver