The cupra and FR's run the same engines, the major differances are that the Cupra has a bigger turbo, bigger intake and a FMIC, the FR has a smaller intake, SMIC, and smaller turbo, hence why there is a performance differance even at the same outputs.
VAG TDi's be it in a SEAT, Audi, Skoda or VW are all understated in terms to their power. It just must be one of those things. As i said before i would have thought it very unlikly SEAT would deliberately put in the wrong engine.