Out of the box I don't think there's a way to filter templates on a group of objects. One other parameter that is specified in the email template condition is the recipient's email address. You could potentially use different email addresses for the notifications setup in the GUI. I haven't done this myself, but I have noticed that if the email address in my notification rule in the GUI doesn't match the condition I created for the email template it doesn't use my custom template and sends the default email format. So it appears to also use the email address as a filter. This certainly isn't ideal, but if you have the flexibility to create different group emails for each group of objects it might be workable.