I use reversed mouse buttons mapping (for left-handed mouse use), e.g. from xorg.conf.d:
Identifier "mouse catchall"
Option "ButtonMapping" "3 2 1"
When I play freedroidrpg (both 0.16 and 1.0rc2) in the fullscreen mode this setting is ignored and mouse button mapping is reversed to the standard one . But in the windowed mode the system settings are respected (left button is right and right is left).
FreedroidRPG should respect system settings in the fullscreen mode as well.
Alternatively it should be possible to remap mouse buttons the same way it is possible to remap key bindings now. It will be the best to implement both solutions.