Posted October 06, 2022

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.

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.