From my understanding of your question, I think that I've been doing this for quite some time now. I don't use a family table for this operation. First, change color of all part models to white, or any color you choose that would best represent a machined surface. Next, change color of ALL SURFACES of each part to a different color. What this does is show the machined surfaces in a different color so you can differentiate more easily. It's kinda like peeling a potato! Then, create the unmachined assembly and save it as a part number. With your new assembly, create the machined cuts and the white surfaces are then revealed. With all your assembly cuts in, save this new assembly as a new part number.
This way when you create your bom on your unmachined assembly drawing, it will include all the parts that went into the assembly. And when you create the machined assembly drawing, it will include just the unmachined assembly with all the machining processes.
Hope this helps. It's worked for me for years without any worries. I don't use Intralink, just a folder for all parts and assemblies.
Best Regards,
Jason