I absolutely agree, there's no logical reason to disable achievements by using mods, as they're easy to get in plethora of ways other than "the vanilla way" even for the most casual of users, Cheathappens, Cheat engine, loading save profiles, you name it.
I'm just arguing thoughts that would perhaps make sense to someone who is against enabling mods and achievements (for what ever odd reason). It boils down to either about creator's pride, "I won't allow you to play my game and get the treats if you alter my fantastic creation in any way!", which as you all point out, doesn't really accomplish anything on their end...
Or it boils down to some API between the game and Steam, that files in a particular folder structure is "applied" to the Steam achievements API and anything beyond that is considered a "cheat" for a lack of a better term by the achievement API and won't trigger, which would explain why that you can make mods compatible with achievements by moving most of the mod's files and folders into the standard corresponding directories of DoS2, and there's not actually anything Larian can do about it other than relying on us to find workarounds, like FNIS for Skyrim etc. If that's the case, I have no idea. No clue how steam and their achievements work.
So yeah... That's pretty much the only two reasons I could guess why mods aren't enabled with achievements.
