I think it's on-purpose to not disclose the answers to those questions. Very similar to the real life, where humans will most likely never know the answers to their own origins.

I think this article is nonsense. Although at the end of prometheus, there were no eggs left in the Engineer's ship, there was an alien, likely the queen, born out of the Engineer at the end. The eggs seen in original Alien were most likely laid by this alien. If every answer needs to be specifically described in the movie, then the movie becomes too straightforward and there's nothing left to perception of the audience. Likewise most of Nolan's movies leave a lot of questions unanswered on purpose.