Surely local juristiction would hold sway over Ryanair, they cannot legally enforce their Irish T & C's in other European countries.
So if a country decides you can take live pigs onto a flight then every airline must agree to it !! An extreme example but just as valid.
Spanish are taking this viewpoint because they say they are not taking as much money as they like at their airports.........I doubt EU will go along with this even if it gets that far.