xserver also has a way to do so: (https://lists.x.org/archives/xorg/2016-May/058039.html)
May 7 2016
May 5 2016
@ Campbell Barton
In the Mir display manager this can be achieved by using (https://unity.ubuntu.com/mir/struct_mir_display_output.html).
In the Wayland display manager this can be achieved by using (https://wayland.freedesktop.org/docs/html/apa.html#protocol-spec-wl_output).
May 4 2016
I have just started a conversation about it on the Freedesktop mailing list. As soon as we get some conclusion, I will post it here.
Apr 28 2016
Seems than your point is right, and the only way to configure that right now is per desktop environment.
Apr 27 2016
Also reported to (https://bugs.launchpad.net/ubuntu/+source/blender/+bug/1575703).