Each Bethesda game since Oblivion has had a script extender and allows modders to go above and beyond even the GECK to create mods. If you are unfamiliar with Fallout 4 Script Extender, it is a product from a team that is the heart behind some of the greatest mods for Bethesda games. When you use the launcher it overwrites your mod settings (I've heard even if you have it set to read-only) With the script extender you get the advantage of skipping the intro videos, and you don't have to fiddle with NMM everytime you want to launch the game. The easiest solution I've found is to install Fallout 4 Script Extender and launch that instead of the main launcher. I'm seeing a lot of people talk about how the new patch disables mods, and a lot of people are posting to start the launcher, then go into Nexus Mod Manager re-enable the mods, then press play but there is an even easier method: But here is an easy way of dealing with it, if the new patch breaks your mod support:

I posted this on Reddit, because I dealt with it during the beta patch.

Fallout 4 mod skip intro