Ticket Price
 

16:00 Dublin/Cork on 25th Returning on 09:30 on 28th costs €71 online.

Im heading for the weekend hence the query, you can however purchase the Waterford / Cork via Heuston for €42.50. Same trains.

25th
13:00 Waterford - Heuston
16:00 Heuston - Cork

28th
09:30 Cork - Heuston
13:20 Heuston - Waterford

As both legs require a change at Heuston, Im guessing it would be almost impossible for ticket checkers etc to determine if I had arrived on the Waterford Train and also, If I will be connecting to the Waterford Train on the return.

Omitting to travel on the Waterford train is strictly speaking a violation of CIÉ bylaw 6. In practice it is highly unlikely that you will be challenged as long as you carry a printed copy of your itinerary with you.