The SJ ship in Prometheus may not be the Derelict ship on LV-426: the ships are both clearly from the same source-creator, but are different 'models', if you will. Like how a Toyota Camry isn't the same thing as a Toyota Corolla, but both are made by Toyota. The SJ Chamber in the Derelict is much larger than the SJ ship in Prometheus, though it could be argued that the SJ Chamber in Prometheus is just another part of the ship Dallas and Co. never got around to seeing, due to Kane's 'accident'.
So really, what's going on with Prometheus is that it's clearly set in the same universe as ALIEN, and touches on at least two topics present in ALIEN (the Space Jockey and Weyland Co.), while also expanding on the universe. It's been pointed out for a while now that "what if the xenomorphs were actually at the bottom of the food chain on their homeworld?" We could very well end up seeing creatures even more menacing in Prometheus or potential sequels to Prometheus that make the xenomorphs mere child's play in comparison.