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.Keys: What I did here and fixed all problems for me was literally copy the plugin.txt from:

Mod Organizer 2/profiles/Default/plugins.txt

to

%username%\AppData\Local\Skyrim Special Edition GOG\

And mods started working fine.

Remember though that if you use SKSE64 - GOG, you need to open the game through skse64_loader.exe for your mods to be loaded.
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DDDespair: Thanks. Now racemenu and most of my cosmetic mods work.
No problem! :)
Searching for mods in Nexus Mods someone made a script pointing out that we also need to copy 'loadorder.txt' from the same folder to AppData\Local\Skyrim Special Edition GOG for Mod Organizer 2 load order to be applied.