I understand that passage on the K-D line in free as part of your day with a German rail or other pass. My question is do you go to the ticket and they give you a free ticket or what?
From the Eurail website on German pass benefits,
"Currently, the Eurail discount is only available in person. Present your Eurail pass at the dock when you make your reservation."
Regardless, I would ask first at the ticket kiosk while you are waiting for the boat. They will probably accept the pass for entry to the boat, but it makes sense to check in advance.
Note that to using the pass for boat travel that day, along with any train travel, consumes a day of the pass.