Regarding the xenomorph mural in Prometheus, I think the only reason that it's in the movie is because it was made for a previous version of the script in which the creature already existed in its final form, and that they didn't bother to replace it as a lot of work probably went into it and they were not even sure where they would be going with the story in possible sequels.
However, if after the next few movies in this series EVERYTHING (who knows, maybe they did have an ingenious master plan!) in Prometheus makes sense, I will eat my hat and post pictures of me doing so.