The problem with that "middlergound" is: why would developers care if players cheat on their game?
This is not an MMO or a competitive game, one player cheating doesn't ruin another player's experience.
Not to mention that if someone actually wants to cheat achievements there's absolutelly nothing Larian can do about it. Cheat engine is MUCH more efficient than any of the mods currently available.
I could go even further, one could download a savegame right before the achievement trigger (I personally have some for the currently bugged achievements, only I checked a list of achievements and rushed there myself, still, I could give them to someone else)
The conclusion is: preventing a modded game from getting achievements does absolutely nothing to prevent achievements from being obtained by cheaters but it does prevent people who want to improve their gaming experience from gaining them.
I don't actually know why people even care about cheaters (and this is not in anyway related to mods, even though some argue it is) getting achievements anyway. Personally I don't feel insecure if someone else gets a hard achievement with no effort, if anything they're the ones missing out on the fun of getting it.
This limitation should definitely be removed, it doesn't have a place in a game advertised as mod friendly (and also the reasons listed above).