Although the planet/moon from Alien is meant to be in the same solar system.

One theory that is going around is that the ship from Alien predates the ships seen in Prometheus. That it contained all of the engineers alien eggs/samples and was lost/crashed when some of the aliens escaped. What we see in Prometheus is the engineers' attempts to re-create the aliens through biological experimentation. Hence the mural/altar to the alien in the ampule chamber.