I can't get mods to work without this file.
You dont need this file to make mod (loose files) to work. The Fallout4custom.ini is nothing special, it is just an override to the fallout4.ini. Basically you can have the same ini settings in both files, but the Fallout4custom.ini have a higher priority, so everthing that is in both inis gets overriden by the setting in the Fallout4custom.ini.
- the Fallout4custom.ini is created with the start of the game Fallout4.exe
- you dont need Fallout4custom.ini to make loose file mods work
- the massage you get from NMM is just a general warning massage. The NMM only scans the Fallout4custom.ini and ignoring the fallout4.ini settings. So if you have modified the necessary items, NMM will keep nagging, But you can ignore it.
- you can apply the ini modifiaction also to the fallout4.ini and it will work
Or you can use my tool to enable mods as loose files, it will do the ini modification automatically.
I will upload an updated version later today, to fix the NMM nagging.