Quarantine entire message and replace with text (By part for Store) will quarantine the entire .msg file during a transport scan. During a scan of the store (Auto-Protect, Background scan, Manual Scan or Scheduled scan) the message will be quarantined by part. The message body and any attachments will be separate items in quarantine. This is due to the methods SMSMSE uses to access the Exchange information store, the APIs used to access the Exchange information store only allow SMSMSE to see the message as individual parts, rather than a full .msg file. During Transport scans, SMSMSE sees the entire message as an .msg file.
Quarantine attachment/message body and replace with text will always result in items being quarantined as seperate parts, regardless of the type of scan that detected the content filtering violation.