Across LE Internal Transfer SFO-how to generate Intercom. AR Invoice with multiple Ship to locations

Summary: As per our client requirement we are using Inter Org Transfer- In Transit for Inventory movement and as it is between two different LE, SFO is also configured and SFO is generating the AR and AP Invoice. We have defined the sending entity as Supplier and receiving entity as Customer, but the customer have multiple ship to locations and it is not always only one ship to Location and so if we define multiple customer sites for multiple ship to Locations and how do the SFO recognize which customer site to be picked for generating the Ship to and Bill to