Currently a lot of settings are gome from mate-control-center. It is just a nature of wayland - only compositor can control those things.
Mate wayland session currently is created for use with wayfire - so here we can go more and in those cappplets that are not compatible with wayland and currently just do nothing insert a check - if under X - work as expected, if under wayland - call wcm. F/e for mouse/leyboard settings we can simply call wcm -p input