It also says many times otherwise in the game that Vegnagun was built specifically to combat Sin, including the entirety of the first and second chapter. Like I'm going to believe the biased opinion of an old-undead man whose reliability of words after FFX-2 were put in definite suspicion.

FFX-2 also has a bunch of plotholes that directly contradict that which was said in FFX, but hey, I've only played the game seventy damned times.