I have Doom 3 and Doom 3 BFG edition in my GOG library. I received the game for free through a promotion. I am unable to add Doom 3 Phobos to my library because the checkout process requires that I own the base game listed on the store. In other words, I cannot add the free mod to my library despite having the required game. This should be changed so it checks against users' libraries for the game, too, so that people who have the game through a promotion can use the free GOG Mods. Thanks.

There is a second oversight in a similar vein to that one. Clicking "See all GOG Mods" to browse all available mods takes you to this page, which is the entire catalogue reduced by the tag "Mod." Given there are only seven available presently, this is okay.
But if there were pages of them, it would be much more tedious. There is no way to refine these results for mods for "games I own" or "games I wish to own." Mods also don't count as "DLCs or extras" (yet), so they aren't made visible or hidden as one might expect. In other words, they aren't properly associated with their parent game with regards to the catalogue's classification system. So they only way to know if a game you own has a mod is to manually search for each game you wish to check, or sift through them all.
Gamesieve will (probably) do it better once that chap gets around to adding mods.

*g* I'm aiming for Thursday, since I'm swamped the next couple of days. Until then, I've made these show up as expansions, so that they at least group with the correct base game.

Oh, you don't need to worry about explaining yourself to someone like me, I don't hold "some person doing the community a favour in their free time" to the same expectations as a company whose responsibility it is to have such things in order alongside the release. Thanks for your efforts.

The way GOG implemented these mods as I understand it, is wearing their hat on their bottom and their trousers on the head. Instead of a little patch (or not so little if it's a total conversion), you get the whole game with the mod preapplied.

So that will definitely change how other mod installers detect the game, and will be worse than redundant and/or useless for games like Starbound and Civ IV, where their entire engines are modular.

Or games like RCT2? OpenRCT2 has a content manager and new/improved content, plus the mods would be absurdly numerous and tiny!

Plus I can imagine some modders specifically coding exceptions for the GOG version because of past mistakes GOG has made.

I can't see this way endearing itself to modders, especially if GOG forgot to ask.
AGAIN.

Quite funny actually that they've tagged Enderal, but not Nehrim. Ergo, there's more, but they got missed. Not sure if it was by accident or on purpose, but this is GOG, so probably the former.

I'm of the firm belief this whole thing will be a painful lesson for GOG.

Let people mod games the way they want, and do not get involved.
Say you have a modder who has been making mods for decades. Now, add to this the thousands of modders who have used this modder's work in their mods. You are leaping into a minefield of conflicts, duplications and complaints, not to mention any legal repercussions that arise later.

I agree. Probably there are more free mods out in the catalog that are not listed as "mods".
The fact that mods could already be in the package but not activated bugs me quite a lot. It means it's a bit like with "premium content that's already there" games: I download for example six characters but, unless I (insert conditions, from "click a button" to "dance at midnight in the moonlight") I can only play with 5 of them :(

Yeah, agree with the oversight and that there definitely needs to be more categories for the mods.

Currently there are only 7 but 6 seem to be unofficial content expansions to further bolster the game (Fallout London, Doom 3 Phobos) and one "fix" mode for Vampire the Masquerade. In the future, you would want these to be separate and also maybe even divide them by game type and franchise.

I am excited to see what sort of Witcher/CyberPunk mods CDPR approves or likes that they add to their mod library.

I just released my initial implementation for modded games on gamesieve.

It is not a mod library, it is a modded games library (i.e. yuu do not get the mods themselves)

Are there any total converstion mods for either the Witcher games or Cyberpunk: 2077?

No. I think the closest was the various graphical update and balance patches that CDPR incorporated into the Witcher 3 4.0 update which changed quite a few things (like significantly nerfed food, made combat and builds easier, etc.) I think some fans have worked on making additional quests for Witcher 3 like one for Blood and Wine similar to the first W3 trailer where Geralt fights the succubus.

Maybe doesnt fit the term of "total conversion" but there is content expansion attempt for Witcher 3 ro restore cut content and items that seems to be quite heavy. Main ones I found are new and original quests.