yes, anything fulfilled on the one item fulfillment record will appear in the email if you configure it this way..
so, you could fulfill line by line, each line will get its own IF record and therefore its own email. or you can decide to fulfill all lines at once too, and then they would all appear on one email.
One thing to consider is if you are utilizing multi line shipping on your sales orders - if you have an order with a lot of shipping addresses, this can result in a ton of emails going out when the IFs are created, so I would suggest making your workflow only work when the Created From record ismultishipto field is set to F. in these cases, my company utilizes a saved search to generate an excel sheet with each addr & tracking # and manually has a CS rep send the attachment to the customer so we don't spam them.