Now that it is pretty much proven McAllister is RJ, here is how I think he escaped the explosion:

http://o1311.hizliresim.com/1h/l/unkm2.jpg


We all know that the bodies found were not exactly recognizable due to the explosion, however DNA showed 3 matches. With no McAllister visibly running around, safe to assume he is dead.

However, he did get away, leaving some sort of DNA behind. CBI would think he was blown into pieces and thus they wouldn't need a body. He was the first one up and out of the house, he ran off. Bertram meanwhile took the heat for being RJ, this brought the real RJ out for ego reasons.

Meanwhile that cup breaking gave Jane the idea of pieces. CBI assumed that only pieces of McAllister were left, while really nothing significant truly was.