I think that the ExternalID was more designed by XMPie, to make data exchange easier, between uStore and a 3rd party application.
Indeed, most entities in uStore may have their counterpart in 3rd party applications (a store, a user, a product, a product property, etc.) but the ID of these entities may differ, between uStore and the 3rd party application.
Per instance: the ID of the uStore product "Letterhead" is 123 (you cannot chose this, as it's automatically calculated by the SQL database), which does not mean nothing in your MIS, where the very same product is identified by "LH999". Assigning "LH999" to the ExternalID field of uStore product 123 will let XMPie export this information in any XML document, that the MIS can process.
That being said, if no 3rd party application does exist in your context, you are certainly free to use the uStore ExternalID field for any other purpose.