There was actually someone who asked about a self-destruct mechanism being at the end of the film and there was a sort of 'no comment' attitude in the answer. Quite whether that means it was in one of the drafts, might be a red herring they want to set up or something else, who could say? Bridging the two films together, I don't see as anything like a problem. They said that about the previous one, too, but it ultimately turned out to be something alluded to, rather than anything else. The novel said as much as the film about the beacon: The Nostromo crew assumed it was a warning, but after only a few hours of Ripley spending more time on it, she was the one who said it then looked like a warning. I would imagine that a professional team of cryptologists would have even earlier success! Nowhere was it said, outside of Ripley Scott's mind, that they were definitely a biological weapon, much less whether they were manufactured or just naturally discovered. Ash only spoke about the ship not being like anything seen before and, considering when he said it (while still maintaining cover), could have been lying. Again, I've done scripts in well under a month. Under a week, even. Simply tweaknig someone else's work, already in place, would be even quicker! Heck, I could have done over the last film's script in well under a week and improved it by a very large degree.