The 12 magic sites were mentioned during the Chao incident. They're likely tied to gates. I'm betting the inactive one in the ruins of Ostia is linked to an inactive gate in the ruins of old Mahora Academy, under the World Tree. Negi probably went to the gate in Britain because it was the closest _active_ one at the time.
We don't have much detail about the gate system. For all we know, one gate can link to multiple gates on the other side. What I'm curious about, is if Time moves the same on both sides, or if it's relative time like Evangeline's resort. It would make the whole "we're late for the next school session" problem disappear.
By the way, people from Mundus Vetus (Old World) are called "Veteres" (c197)