setxkbmap cz -variant qwerty fails, only unmodified czech keyboard works. It's a small problem in includes within /usr/share/X11/xkb/symbols/pc/cz. Reported and solved in the upstream bugzilla https://bugs.freedesktop.org/show_bug.cgi?id=7778 but rejected since the package is no longer maintained upstream.
*** This bug has been marked as a duplicate of 157828 ***
Dupe.