My guess is there's a check in the engine for specific information in the meta data of the main game and if something is sitting on top of it cheevos are disabled.
If I'm remembering/understanding right, the Skyrim achievement enabler required a DLL loader and SKSE, which basically means it got injected into the exe and modified the memory to enable achievements - It wasn't actually a "
normal" mod. So we may be in similar situation, unless Larian changes it in the coming months.
