I have never, not ever, launched fallout 4 without mods already being installed. I may have launched the game once through steam...but that was by accident and I quickly shut it down and opened it proper with F4SE. I'm not sure why you don't want the assistance of a mod manager/organizer but to each their own...with my 255 mods...I wouldn't dare tackle load order from scratch. Good luck and hope this helps.
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![Is getting Fallout 4 to manually run mods possible? Osoksi10](https://i.servimg.com/u/f97/19/54/55/26/osoksi10.png)