Vergil's part of the story is indeed a prequel.
From the Official Website: Vergil is Dante's twin brother, and he also carries the bloodline of Sparda. Unlike Dante, he embraces his demonic heritage. Intrigued by the Order of the Sword, who worship Sparda as a god, he pays a visit to Fortuna many years before Dante's arrival.
So, Vergil's in Fortuna years before the events of DMC4. That could mean that the Special Edition is depicting events between his disappearance in DMC3 and his death in DMC1, or before DMC3 entirely.
Also, I saw these on the Japanese website:
Some kind of pre-order bonus...so take that for what you will.
SO IT'S IN THE PAST
AND VERGIL HAS A STORY !!!!!