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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