I'm not quite sure Steam itself has something against it, since there are plenty of games that do not require any workaround to have achievements work with mods, even from the workshop (Darkest Dungeon, X-Com and Binding of Isaac are probably the more well known examples). On the other hand, Bethesda is pretty adamant on being mod friendly and their games require achievement enablers, which is rather weird.
The conclusion one could reach is that Steam defaults to only allowing achievements on the unmoded game, unless the developers ask for it to not be like that (though this makes the Bethesda case really weird).
I used to think that Steam defaulted to only allowing achievements if the files validated correctly, but Divinity 2 itself awards achievements if loose files are altered, you just can't use the .pak files themselves so...
Another possibility is that the game needs to have some kind of file that "tells" steam to allow such a thing, this option would consider that games like Darkest Dungeon, X-com, and BoI have that by default.
I want to believe that Larian just forgot to ask Steam to allow them on a modded game (just because it's the simpler option). Although only time will tell if that is the case.
