An email message is comprised of headers and body content. When a message is transmitted, the whole thing (headers and body) is wrapped in an envelope. The envelope specifies what system is transmitting the mail, who it is from and who it is being sent to.
When automatic replies are sent from Office 365, MAIL FROM: information for the envelope is set to <> - i.e. there is no MAIL FROM: information.
This means that automatic replies trigger an exception in the transport rule that identifies messages to send to the Exclaimer Cloud - these messages are not routed to the Exclaimer Cloud and so no signature is applied.
Exclaimer will be reviewing how to implement signatures for automatic replies in a future version of Exclaimer Cloud - Signatures for Office 365.