I feel like it would be trivial to include a MO ini tweaks file for future releases. I'm certain myself and Gribble have done this and know that it works, and I believe Jax has tried it as well (he created the sample file.)
The desired output would be to just add the file to the 'Main Files' folder after running the installer, as it's often simpler to rename that to TTW Main Files and drop it in MO/Mods than building FOMODs and installing through MO.
Another note: The MO FOMOD installer is based on NMM's FOMOD installer. As such it doesn't really work for large files.