I think you can justify the partitioned off area to an auditor. One plant I worked at did pasteurization of dried herbs and powders in a walled off area of our warehouse, and on the other side of the wall we did third party storage for a separate business (same owners) of numerous nasty non-food items (from children's toys to pool cleaners). Our facility map clearly designated the food area vs the non-food areas, and employees were trained on the difference. There was a shared loading dock for the warehouse, but we justified it by demonstrating no food products were ever opened outside of the food treatment area.
I'm not up to speed on GFSI requirements for packaging manufacturers, but I'd say any program that applies to the building will need to encompass the entire building and not just the food-grade area. In our plan, for example, the whole warehouse was under pest control monitoring and auditing (since getting the mice and rats to sit through a GMP training to stay out of the food area proved impossible). We also covered the entire building with our food defense/security requirements, sanitation program had to cover the shared dock/loading area, etc. If you can demonstrate to an auditor that the packaging can be made in compliance with the code, and that the non-food area does not pose a risk to the food-packaging, you should be able to work something out.