The new version has remapping buttons option?
There is still no GUI for remapping buttons. You can do it from Tcl, but since the Zero doesn't have a keyboard that means messing with scripts.
There is an OSD keyboard you can call up with SELECT, which allows you to press MSX keys. That works if you don't need to press a key very often, for example if you want to press "1" to start a 1-player game with joystick in old Konami titles.