The MCM has been released for Fallout 4 and has a few issues with MO2. Mainly mods not showing up in the menu. This can be overcome by creating an MCM menu in the vanilla games data folder and copying each mods MCM there.
After any hotkeys are set the resulting output will be written to the overwrite folder and a mod can be created from this and enabled. Any subsequent changes to the hotkeys will be written here. You may see another empty folder in the overwrite foldet the first time this is done.
Tested with MO 2.0.7.