Hello howtobuild-plans -
Unfortunately, there are no additional filters for Auto-emails. While you can set the conditions, where available, for auto email to be sent, there is no ability to exclude certain items from the trigger for the event. So, for example, if you have an email set to be sent when an item has shipped, any time that changes on the eBay sales page so that the item shows as shipped, the email associated will be sent regardless of which item that is.
However, I can see how such a feature may be useful and have forwarded your idea along as a feature request to our Product Management team for their consideration.