You can easily store the same ‘item’ in different packs. These would be simple sub-recipes, which would take a certain amount of a batch recipe. The name would correspond to the pack size.
As an example:
You create large batches of marinara in a commissary, and package them in 1 gal bags to send the stores. Those bag recipes are simply quantities of the marinara (you can also price out the bag). At the store, the bag is opened, and either
1. Portioned into different selling units (6oz, 12 oz) as prep recipes, or
2. Ladled onto serving recipes (e.g., eggplant parmesan sandwich)
You can count and manage these at any point during the process, e.g., count the entire batch, the gallon bags, the portioning containers, etc.