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This worked! Thank you
I feel like an idiot now lol
Turns out going into \Mod Organizer\Fallout 4\profiles\Default and manually deleting the fallout 4, custom, and prefs ini folders and relaunching again through MO also works because it copies the settings from the vanilla files. It's weird that MO has it's own setting files for the game, and doesn't just use the ones that are already in the vanilla Fallout 4 files.
You need to read other information about the update, hotfix, and F4SE's changes, as well as anything from Mod Organizer 2. I wouldn't expect MO to be updated to accommodate the game's changes.
This thread is super old, and has nothing to do with your current problem.