Thank you, my dude! I dislike Vortex a lot, and this actually helped me, I just copy-pasted files created by MO2 into this folder, and indeed - there was no set mods there, at all! But putting those copied files made Alternate Start mod run correctly ^^

Yeah, that was my intial guess too, and I got my mods to load. Still, there seems to be a problem with SKSE for me. All mods that rely on it complain about SKSE not running. I have downloaded the explicit GOG release. Could it be that the executable differs from other Anniversary releases?

As you can see on the SKSE site,
Current Anniversary Edition build 2.2.2 (game version 1.6.640)
Current GOG Anniversary Edition build 2.2.2 (game version 1.6.659)
Current Special Edition build 2.0.20 (game version 1.5.97) - you probably want the AE build above unless you know what you are doing

The GOG version differs from the rest and it requires a specific SKSE version made for it. It doesn't help make things less confusing that there's actually only one base game on GOG and that shows up as the Special Edition in your library, while the Anniversary Edition just has a DLC package as well.

Thanks for the quick response. Sadly, I do know about the (yes, a bit confusing) versioning and that both SE and AE on GOG are actually the same build. Checking the executable and having spotted the GOG release of SKSE 2.2.2 (1.6.659) left me with only one option anyway.
SKSE still doesn't run, hence mods keep complaining and do not load entirely. Rest assured, I am well-acquainted with Skyrim's file/data structure and I have never experienced any problems with manually setting up mods so far. It remains a bit of a mystery.

Just got the Special Edition. Yer telling me that SKSE for AE will not work with SE?? (in the middle of downloading, can't test atm).

Only things I can think of.
1: The files are in the wrong place.
skse64_1_6_659.dll and skse64_loader.exe go in your main Skyrim Special Edition folder and the scripts folder goes inside the Skyrim Special Edition\data folder.

2: You are starting the game with the launcher and not skse64_loader.exe.

Does SKSE give you an error message when you run SKSE64_loader.exe?

You need to get the GOG Anniversary Edition Build http://skse.silverlock.org/

Thanks man, sometimes a small detail is oft overlooked. Appreciate the information.

I can't guarantee this is accurate for you. But when the game is installed it looks for a specific directory to find the ESM/ESP files at. If you copied your game to say a ramdrive or moved the directory, it identifying what mods are available may be wrong. (And if you have say a Steam version AND GoG version, who knows which directory it is looking at, unless you edit it in regedit)

Otherwise if the mod manager isn't doing the job, you might try the launcher, and select the mods which will update the plugins.txt file(s).

But if you did a clean install recently i doubt this issue will crop up.

1: Yep.
2: Yep.

SkyUI and RaceMenu both complain about SKSE not running (version 0.0.0.0).

The first thing that seemed way off was that Skyrim's GOG release did not create a LoadOrder.txt and Plugins.txt within the %LocalAppData% folder at startup--I had to create and fill in those manually. Plus, said %LocalAppData% folder is named "Skyrim Special Edition GOG" (note the GOG appendix) and may indicate that GOG has actively altered the executable and/or additional files, which seems logical when considering the removal of any DRM code.

At least for me atm. Yet, note that both SE and AE from GOG seem to be the very same build (1.6.659), with an assorted mod pack for the latter being the only difference.

Gonna check some things later after work and get back to you.

(EDIT)
I did check administrator rights--to no avail.

Will Skyrim get it's separate forum? I feel that it should get it's own forum

===> Separate vgame subforums for The Elder Scrolls series. Pros? Cons?

SKSE and SkyUI are working now, albeit with one exception. As it turns out, RaceMenu's skee64.dll is not compatible with the GOG-tailored release of SKSE.

Manually setting up custom mod packs really makes troubleshooting quite the hassle.

https://www.gog.com/forum/general/release_the_elder_scrolls_v_skyrim_79ad7/post540

As an update to this post I made:

Tried to test Vortex but noticed it's almost fully dependant on an Online connection for resolving problems and troubleshoting it seemed to me. If Im wrong, please correct me. With all due respect to Vortex developers and their work, I can't use this. I only play my games in a Win10 Offline boot.

So I decided to switch to Mod Organizer 2 and got awesome results using the workahound suggested by Trixx.

Skyrim is running here fine with those mods working well apparently:

Better Dialogue Controls
Carriage And Ferry Travel Overhaul
Cloaks of Skyrim SSE
Enhanced Blood Textures
Immersive Citizens - AI Overhaul
Immersive Weapons
No Spinning Death Animation
Point the Way
SKSE64 v2.2.2 - GOG
SkyUI v5.2 SE
Sounds of Skyrim Complete SE
Unofficial Skyrim Special Edition Patch
3PCO - 3rd Person Camera Overhaul
Amazing Follower Tweaks
Better Message Box Controls
Diverse Dragons Collection SE
Immersive Armors 8.1 SSE
Immersive Patrols Lite (Patrols Only)
Relationship Dialogue Overhaul
Relationship Dialogue Overhaul - Amazing Follower Tweaks Patch
Run for your Lives
Skyrim Weapons Expansion
Weapons of the Third Era

These were tested using Skyrim Special Edition (Without the Anniversary Edition installed.)

I'm still going to test more mods throughout and troubleshoot when I have the time. I'm specially interested in the Dragon mods - as they add and change many things in Skyrim, therefore, high risk mods.

-- Talking about SKSE - GOG Mods: ---

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.
Also remember that this is a workhound, that means that everytime you install a new mod through MO2, you will need to copy Mod Organizer 2/profiles/Default/plugins.txt and update your %username%\AppData\Local\Skyrim Special Edition GOG\plugins.txt mod list.

Until MO2 devs update it to be compatible with GOG paths, manual update of the file is necessary.

Vortex has the same issues... without manually copying loadorder / plugins from the Appdata - Skyrim Special Edition folder to the Skyrim Special Edition GoG folder each time you install a new mod, it wont read any new mods installed since the last time you did. IDK if this is a Game issue or a Vortex issue but its a PIA.

"I guess I'll buy the game on GoG, it will make modding easier" - A fool once said.