Why do all the PDF documents appear in the Vault Viewer even though only one is selected from the email?
This is expected behavior.
The Vault Viewer enables users to access all documents referenced by the Approved Documents (Email Template and Email Fragments) in Vault without returning to the email to select each one individually. This is a default feature of the Vault Viewer and may not be disabled.
CRM Vault Viewer Documentation: Embedding the Vault Viewer in Approved Email Content