I just discovered on x2goserver-4.1.0.3, that if you depclean x11-apps/xkbcomp out of your headless system (vserver), keyboard configurations will fail to work. Clearest symptom: AltGr won't be recognized in X2Go sessions anymore. Looking at deps, `setxkbmap` nor `xkbcomp` is listed anywhere. `/usr/bin/x2gosetkeyboard` uses `setxkbmap` extensively, so it does look like missing dependency definitions.
Possibly related: https://bugs.x2go.org/cgi-bin/bugreport.cgi?bug=1160