Its buried in page 29 of the Terms and Conditions of Travel,
http://www.platform11.org/resources/...riage_2004.pdf
Quote:
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Subject to paragraph 1.2 to facilitate passengers travelling to/from final destinations that are between railway lines ordinary single and return tickets will be interchangeable between adjacent routes as set out in the table below
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Purchased for Valid on routes
Dublin/Cork Dublin Limerick/Tralee/Waterford
All routes are listed
1.2 is the Nenagh branch rules
Return Dublin Cork is €61, return Dublin Millstreet is €61
So you are fine. If you meet a ignorant ticket checker be sure to take names