There's three rugby teams that will be using the Thomond pitch; Munster, Bohemians and Shannon - so it's not necessarily the case that that Thomond would be available to host the final and even so, getting the pitch ready for a football match in November could be troublesome.
Both venues have there pros and cons but ultimately the location of the teams involved should dictate where the final takes place. If the FAI have this flexibility open to them, ie both the RDS and Thomond are available, they should by all means use it. If not, they should focus on hosting in the RDS.