If you look very, very, very closely you can see the shadow of another guitarist behind the stack, I would know I saw at warped tour
Yes, they do have a third guitarist, which Matt C. did for a while and now it is Bryan Donahue. But for the live performances of Dear Maria, Flyzik and whoever is the third guitarist will step off stage, and the band plays as a true four-piece with no backing tracks added. Then at the bridge, when they are playing to an actual crowd, Alex and Jack will throw their guitars to Danny and Flyzik, and go into the crowd. So for this performance, because it is a recorded performance, they play Dear Maria, the whole way through, as a four-piece.