It is probably possible to make item movement on belts parallel, but other components aren't so simple to parallelize so issues could arise from the interactions between the objects in the world. This can be fixed by computing all items at the same time before anything else each frame. It is also possible to make parts of the code run in parallel, like the collision detection function for the items, and the code inside crafters that checks their inventory against the recipe array. The problem is that the functions in gms2 aren't programmed to run on the gpu, and I don't think gms2 has an option to make my own code that runs on the gpu (apart from the shaders), so I would have to make my own engine for that.
If I was to write my own engine, I would probably try to have all the objects in the world compute in parallel in relation to the same world state (and not in order, updating the world one object at a time like how gms2 computes it), which would open up the possibility of running a lot of it on the gpu, but I think I would have to program everything in the game in a very different way, and I don't have much experience actually writing gpu programs anyway (my experience is limited to the colour replacing frag shaders that the cowgirls use to render). I also don't know how well object oriented stuff works with the gpu.
You are right that parallelization would be good for running a game like this, but I am not experienced enough to make it happen sadly.