The game stores your load list in a text file already. It is called plugins.txt. It can be found at AppData\Local\Fallout4. This is the file the game reads to know what mods to load.
CAUTION. If this file is trashed, your game is trashed.
I mod Fallout 4 manually. I only use NMM for complex FOMOD mods like CBBE. Out of 192 esp mods I have installed only 3 were through NMM.
The plugins.txt file does not care if you add the mod manually, use NMM, the in game install or a combination of all 3(plus any other mod organizer) . If it isn't on the plugins.txt file the mod will not load.