I have a yoga 2 pro which doesn't have a working accelerometer driver. As such, if I want to rotate the screen I need to use gnome-control-center.

Unfortunately, when I do this the touchscreen input coordinates also don't get rotated.

I tracked down how this works:

apply_current_configuration() in gnome-control-center/panels/display/cc-display-panel.c calls 
gnome_rr_config_apply_persistent() in gnome-desktop/libgnome-desktop/gnome-rr-config.c calls
meta_dbus_display_config_call_apply_configuration_sync() in gnome-desktop/libgnome-desktop/gnome-rr.c calls (I think)
meta_monitor_manager_xrandr_apply_configuration() in mutter/src/core/monitor-xrandr.c

The last call is what actually does the XRR calls as far as I can tell, and it does not do any XChangeDeviceProperty() calls regarding the Coordinate Transformation Matrix.

Fortunately, the xrandr plugin in gnome-settings-daemon DOES handle rotating touchscreen coordinates (in rotate_touchscreens() in gnome-settings-daemon/plugins/xrandr/gsd-xrandr-manager.c). Unfortunately, this code is only triggered on XF86RoateWindows key event(sp?), and not from g-c-c, gnome-rr, or mutter.

I'm not sure where this bug ought to go, I'm not sure what there can be done to consolidate the similar xrandr code in g-s-d and mutter, and I have no idea how this will work for wayland, but hopefully someone who's more knowledgeable about how all these parts fit together will have some ideas.
Thanks!