$ sudo chmod 444 /etc/X11/xorg.conf
$ sudo chattr +i /etc/X11/xorg.conf
That fix didn't work for me, ended up killing my keyboard.
What did end up working however was disabling onboard graphics and running it as a headless node.
The issue was that it was being overwritten when the HDMI cable was plugged into the IGFX (intel graphics, motherboard) HDMI port. Ubuntu 16.04 would detect this and mark it as a "Intel Hybrid System" (could be seen in /var/log/gpu-manager.log). Then, it would check the configuration, come up short on the IGFX config and reset the xorg.conf.
To solve this, I went into the BIOS, disabled IGFX, set the default display out to PCIE1, plugged the HDMI cable into the graphics card on PCIE1, then regenerated xorg.conf with nvidia-xconfig -a --cool-bits=28 with no issues.
...
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 1635 G /usr/lib/xorg/Xorg 31MiB |
| 0 2140 G compiz 13MiB |
| 0 24518 C /opt/bminer/bminer 814MiB |
| 1 1635 G /usr/lib/xorg/Xorg 7MiB |
| 1 24518 C /opt/bminer/bminer 665MiB |
| 2 1635 G /usr/lib/xorg/Xorg 7MiB |
| 2 24518 C /opt/bminer/bminer 665MiB |
| 3 1635 G /usr/lib/xorg/Xorg 7MiB |
| 3 24518 C /opt/bminer/bminer 665MiB |
| 4 1635 G /usr/lib/xorg/Xorg 7MiB |
| 4 24518 C /opt/bminer/bminer 665MiB |
| 5 1635 G /usr/lib/xorg/Xorg 7MiB |
| 5 24518 C /opt/bminer/bminer 665MiB |
+-----------------------------------------------------------------------------+