Just Some Thoughts On Prometheus (Not A Review)

Just a few thoughts on the film...  First of all it's a first rate Ridley Scott film!  I'm a big fan of his directing, though I do not think he is a completely genius film maker; one needs only watch Black Rain to get that he has his hits and misses.  The film's story, plot and action are all very interconnective and very well done, except in parts.  I saw in 2D because all the other Alien films I have seen where 2D, though I admit I've only seen 1 in the thearter.  OK, I warn spoilers on this blog, but don't actually spoil much.  Here I am.  It is a well known sequence in Alien that the ship that the crew of the mining ship Nostromo finds has a pilot petrified to the chair of an alien looking ship, notably the pilots chest is ripped out.  Yet in the ending of Prometheus, where the one "Engineer" that is still alive is nowhere near the chair, with what we now know is a breathing mask on, when the first recognizable "alien" emerges from his chest.  Granted, the film makes it clear that there are many ships on the planet.... but, there is only one that crashes.  So, how does the alien engineer of the human species go from having his chest ripped out in a human made crashed life ship, to being the petrified alien captain in the chair found later?  Couldn't Scott have had him hobble back to the ship and try to take off again??  Also, in Alien, the crew finally deciphers what they thought was a transmission worth checking out, which turns out to be a warning beacon not to approach the planet.  Viewing Alien, it's obvious that the warning must certainly was issued by the alien ship that the Nostromo crew found there; nothing is heard at the ending of Prometheus to explain the beacon--again, couldn't Scott have had Elizabeth Shaw (Noomi Repace) issue that beacon as part of her "Ripley Speech" at the in of the film??  I'm a huge fan of both Ridley Scott and the Alien franchise, so, as a fan, I've had a lot of questions over the years about the origins of the creatures and where they came from.  Now, apparently, that's been solved--they were engineered and their home planet was the very "ball" that the Nostromo crew landed on.  I just don't completely understand how a film maker who can be such an artist would leave such blaring inconsistencies in his own work.  I do plan to see it again, next time in 3D, which I understand is excellent and not over the top--so I'll be looking for answers next time.