Fate/Extra isn't the Fuyuki Grail War.
 The Fuyuki Grail is like the 726th Grail War or some such number. In fact, Waver Velvet (Lord El-Melloi II) actually fought in a second Grail War with Alexander the Great (watch Fate/Zero.) In fact, the Mage's Association considers Grail Wars to be backwater rituals because there are so many.