These additional databases are not included in the elastic pool but are a separate resource, the separate databases associated with the additional server are not in the elastic pool.

By setting them up through the portal, they will automatically be backed up as partner of the portal’s backup activity.

Partners can relocate them to the Elastic Pool via the Azure portal, this however will mean that they will no longer form part of the portals backup processes and will need to be backed up separately by the partner.