Yes you can book on the Mayo line, all services except the 16:15 to Ballina on Friday and the 14:25 Westport Dublin on Sunday, in fact its laziness on IE's part that those exemptions apply.
This is the problem with seat reservations the staff will do just about anything to avoid taking any responsibility, I've had words with a train hostess on the Cork train and even mentioning that I would take the complaint the whole way to the general manager no change
