RuiNtD: MO2 doesn't yet support Skyrim on GOG because Skyrim on GOG saves the
load order to a different folder. Even if you set it to use GOG Skyrim's folder, it will write the load order to the wrong location.
Why would that matter?
MO sets Load Order, not those Vanilla LoadOrder.Txt,/Plugins.Txt,
Set up correctly:
Profile specific INIs, and Saves, MO Auto Generates the other Files on it's own for EACH Profile.
How else can MO Profiles be isolated from Vanilla, or each other?
The change of folders will require manual copying of Vanilla generated Ini's, and other game files to the "Default" Profile in the first instance (Until MO devs add them to the default checklist), then copy the "Default" Profile instead of creating a "New" one. Note: I've always made "Defaultt" = Vanilla First, (Leaving Vanilla unchanged), that make Default my "MO Vanilla Source". Then I gather all the must have, always used mods, edit Ini's, to make my Base for every modded Profile.
Those Vanilla LoadOrder.Txt,/Plugins.Txt files should be always showing Vanilla Skyrim without mods.
That way if you load the Game outside MO, you get the Settings files for the Content actually in the Data Folder (Vanilla Game files only). You can even turn all but, Skyrim.esm, and Update.esm into MO Mods by Archiving each Plugin+BSA pairing, as a mod.
I was the most active MO Support Fangirl from 2013-2016. I know exactly how MO works, and what's possible.
MO2 has some differences, but is 90% the same, and Identical for profile management.
GOG is supported by MO2, or to be exact, MO doesn't care about the Store used.
The new folders are an added wrinkle, but not really relevant because MO doesn't alter them when set up correctly.
Sure it takes a little more effort from the user, as with all cutting edge modding, and somebody has to figure out the minor niggles that crop up, and learn how to do things first.