So, before I make the decision of adquiring a DRM-free copy of Skyrim for modding purposes: is this version of the game compatible with Mod Organizer 2?

I don't know how user-friendly Vortex is, but I didn't have the best experience in the past, sicne it seemed to be capped to non-premium Nexus users. I wonder if that's still the case, or if MO2's compatibility for GOG version is even planned.

Thank you in advance.

No, at least not yet.
Apparently the main problem is .DLL and .BIN not loading correctly (.ESP/.ESL/.ESM./BSA seems to work fine).

I recommend keeping an eye on their discord for information on future releases and bugfixes (invite link on Nexus ModOrganizer 2 page).

What's capped is the download speed for nexus downloads. And that also applies to downloads through MO2 (or your browser).

The main difference between MO2 and Vortex is their deployment method. I find managing big load orders a lot easier in MO2 than in Vortex. But given the fact that most SKSE-based plugins don't work with the GoG version (some people say 'yet', others who are less pessimistic, or more informed, say 'most of them probably never will'), your Vortex load order isn't probably going to be too big, anyway. Whether or not the GoG version is supported by MO2 shouldn't be you main concern. Eventually, it will be supported. What's more of a big deal when it comes to modding is the fact that the GoG version is a different build of the game compared to the Steam version. And because of the changes made to the GoG version (no Steam DRM, removal of Creation Club etc.) it will probably never be fully cross-compatible with whatever is the latest build on Steam. That means two things: all modders doing more sophisticated modding of the main executable have to maintain special versions of their mods for the GoG version and in order to do that, they have to have access to the GoG version in the first place.

Meanwhile, quite a few essential SKSE-based plugins haven't even been updated to Anniversary Edition (1.6.x), so if you want maximum mod compatiblity, you do a rollback to version 1.5.97 on Steam (the last version before the release of AE back in November '21). For obvious reasons, that's not going to be possible with the GoG version, even though theoretically, GoG supports easy rollbacks.

To sum it up: as things are now, even though the GoG version should be superior to the Steam version due to the removal of Steam DRM and the Creation Club and the update and rollback capabilities that GoG offers, it's clearly inferior to the Steam version for about 95% of all potential buyers.

I've tested with only 4 mods: SKSE64 specifically for GOG Skyrim version, SkyUI, RaceMenu and ASLAL. SKSE seems to work, yet i had no success with other mentioned mods running through MO2.

EDIT: This is an issue with GOG for whatever reason decided to rename dedicated folders to "Skyrim Special Edition GOG". MO2 can't properply recognize the folders to substitute virtualized profile (ini settings, loadorder.txt and such). What might help (though, i can't be sure it will work with any mod out there) - simply copy your MO2 profile files to:
C:\Users\<YOURUSERNAME>\AppData\Local\Skyrim Special Edition GOG
C:\Users\<YOURUSERNAME>\Documents\My Games\Skyrim Special Edition GOG

And yes, you have to repeatedly do this whenever any changes have been made in MO2, which sucks.

Hmm... It seems to me that it's not GOG that's the problem, but MO2 that has some shortcomings. Linking to new locations should be done by the organizer. GOG cannot use the same location as the Steam version for obvious reasons. Loads of people will use the Steam and GOG version alongside (if only for testing purposes). It would be terribly inconvenient when the Steam and GOG versions used the same locations, overwriting each other's files. That would grow into a mess very fast.

So I guess MO2 has to be adapted to this new situation.

The issue is already being discussed on the MO2 github. Unfortunately, the data paths are hard coded in the game plugin. I really hope the new game plugin will support multiple installs.

PSA: There is an alpha/test version available on MO2 discord right now.
Devs are looking for testers to see if everything is working correctly, discord invite.

Hmm.. A strange choice to make something like that hard coded. I mean - A mod organizer should be a little more flexible than that yes? Anyway - Good to see it's been worked on.

Tried the test version. Works. Now I can at least launch the game through MO2.

Does the test version allow you to manually add the path for your plugins.txt, or just applies it correctly if you have the GOG version?
Just trying to work out if this update will also work for the Epic version, which will likely want the file in a different folder.
As the Epic version seems it will be more like the GOG version than the Steam one.

According to the release notes, the epic version is supported, too. And as far as I can tell, it automatically checks for where to look for the config files for whatever folder you select. I didn't check the code but what was discussed on the MO2 github was a check for Galaxy64.dll to be present in the game folder you select in order for the MO2 client to assume you're using the GoG version (and therefore automatically selecting the correct paths).

Whatever. It just works!

Thanks.

I just checked the official relase after I had used the beta. Now you get a prompt letting you choose your version.