DE using SF Contact ID primary vs secondary email addresses

I created a manual DE using the contact's SF Contact ID and the contact record secondary email address, however upon deployment it pulled in the primary email address. Why did this happen and how can I ensure the address I uploaded in the DE is used rather than the default primary on the associated contact record?

Note this was for a seed list, so I can also create a second contact record for each of these people in my source system. My goal was to ensure each DE I use has a SFID vs email as the ID. 

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