Is there anything missing in an encrypted iPhone backup?
Got answer from Threema support. The keys actually are included in an encrypt iTunes backup but can only be restored to the same device. That is why they advise a separate backup.


  Hello,
  
  Yes, encrypted iOS backups include the iOS keychain and therefore also
  the Threema private key; however as it is stored with
  kSecAttrAccessibleWhenUnlockedThisDeviceOnly, it will additionally be
  encrypted with the device-specific UID key. Therefore, it will only be
  usable if restored to the same device that the backup was created on.
  
  Best Regards,
  
  Threema Support