I am still not 100% sure what your question is, but I'll try to answer as best as I can.
The stretch from Disentis to Andermatt is operated by Matterhorn Gotthard Bahn. According to their website, you will get 25% discount on trains with your Eurail pass. It is possible that this hasn't been updated yet, but I think this is unlikely, as the website below for the other train is maintained by the same company and is updated. The full price of this (before reduction) is CHF 37.20 for a 1st class ticket.
However, there is a special panoramic express train "Glacier Express", operated by the same company with a couple of connections every day. For that train they state on their website that you can travel for free. However, this train has a compulsory reservation charge of CHF 13 during the winter months and CHF 23/33 during the summer months.
I wasn't able to find any information on whether you can buy the ticket for this specific stretch on the train. However in general this is not possible any more in Switzerland and you risk to be fined. Normally you can buy tickets online, but the online system doesn't seem to have the option for a 25% discount. If you don't have time to buy the ticket/reservation in Disentis however, you should be able to buy it at any other train station with a ticket office in Switzerland. (It doesn't need to be from the same train operator)