I got tired of waiting for THQ to fix the GOG version so I took the matter in my own hands. Here is what you need to do in order to play all expansions (Fallen God and Soul Harvest) from the base game (Spellforce 3 Reforced):

1. Install all three games. My install path is "E:\Program Files (x86)\GalaxyClient\Games\SpellForce 3 - Reforced\" but yours could be slightly different.
2. Copy first expansion "SpellForce 3 - Soul Harvest\bin_addons_win32\EXP1_Campaign" folder into the base game ("SpellForce 3 - Reforced\bin_addons_win32\EXP1_Campaign"). Then do the same for DLC_Bavaria folder. You can also copy EXP1_KOR if you want Korean language.
3. Copy second expansion "SpellForce 3 - Fallen God\bin_addons_win32\EXP2_Campaign" folder into the base game ("SpellForce 3 - Reforced\bin_addons_win32\EXP2_Campaign"). You can also copy EXP2_KOR if you want Korean language.
4. After this your "E:\Program Files (x86)\GalaxyClient\Games\SpellForce 3 - Reforced\bin_addons_win32" folder should contain these subfolders: DLC_Bavaria, DLC_DDE, EXP1_Campaign, EXP2_Campaign, SF3_Campaign, SF3_KOR (and optionally EXP1_KOR and EXP2_KOR).
5. Rename file "E:\Program Files (x86)\GalaxyClient\Games\SpellForce 3 - Reforced\wrapper\thqnocfg.dat" into "thqnocfg.dat.bak" (this is for backup, we will override this file in the next step). If something goes wrong then delete the patched file and rename this one back to thqnocfg.dat.
6. Download patched thqnocfg.dat file and save it in base game's "E:\Program Files (x86)\GalaxyClient\Games\SpellForce 3 - Reforced\wrapper\" folder.
7. Done! You can now start the base game and enjoy full functionality with both expansions working properly.

How were you able to modify that file ?

Anyway this works.
But instead of copying files around I just created links to the needed directories, so the expansions stay in their original folders, Galaxy will continue to manage/update those games as always, and there's not the issue of doubling the occupied space.

So, I just followed the points 5 and 6, and then did this (change "C:\Games\" with your base installation folder):

I also created the links for myself but I thought it would be harder to explain to a general gaming public. Besides, these games are not maintained anymore on GOG so it wouldn't really make much difference.

I suppose that there could be issue with online stats, like play time or achievements, since if you start "Fallen God" from the "Reforced", for Galaxy you are playing the "Reforced".

Works great, except it removes the Old Haalâyash scenario. Any way to edit thqnocfg.dat to add it back?

You're right, it's there. I must've been blind yesterday. Thanks!

Does this also work for the expansion factions in skirmish?
Because I wanted to get the game in the summer sale now, but heared I has problems with detecting the expansions and you can't select all the factions in skirmish games.
Can I play Dwarves/DarkElves and Trolls in Reforced skirmishes like this if I got the xpacks?

Thank you so much - I've waited patiently for this to be finally fixed. Works - just tested it, see attachments - the other races are available in Skirmish and matches load normally.
(I've only tested this offline however, don't know about multiplayer.)

Nice
Thanks for testing! :)

I held off on buying the game since the reforced update and how it's not integrated properly and wasn't looking like the dev's even care to fix it. Looks like I might get the game now with this awesome patch.

Good morning,

Yep this worked for me! Thanks for fixing the game Extesy!!! I really appreciate you taking time to resolve this. Make me wish I knew how to do these things.

oh god, thank you very much for your great work, i wait a very long time to play this game complete. thank you!!!

Bravo! Excellent!

I sent the solution directly to the official spellforce 3 discord. And I asked that they now do the necessary since there is a trick to do it officially from the setups added in our library. If they persist in doing nothing then they have the solution in front of them. We can say that the studio treats gog players like big shit.