Does a Process MFG Item Structure have to be defined based on making a singe unit

Have a situation where a client needs to start using an Item Structure with their Process Manufacturing. All new Work Definitions will need to be created for use with the Item Structures. In doing this, does the Item Structure and the Work Definition have to be defined based on a single unit of the primary output? Or can I create the item structure based on a Batch Size of 5000 and a work definition based on Batch of 5000, and if doing so, what would the be the downside effects to costing or work order execution if