ridley scott - How to explain the discrepancies between the end of Prometheus and the beginning of Alien?

At the end of Prometheus, the alien that Elizabeth Shaw extracted from her womb kills the Engineer. Later on, a primary form of alien xenomorph is seen bursting out of the Engineer's chest. The scene takes place in Meredith Vickers' escape pod, stranded at a distance from the Engineers' crashed ship.

At the beginning of Alien, the team that explores the derelict ship discovers the body of an Engineer pilot:

The corpse wears what we now know is some sort of armor, and his chest has been damaged by an alien xenomorph, as we later figure out.

Everything seems to indicate that the corpse in Alien is actually the Engineer in Prometheus. However, there are two major discrepancies:

1. The Engineer is killed in the escape pod, not in his pilot seat.


2. The corpse in Alien is much taller than the Engineer in Prometheus.

What other theory could possibly explain how a (much taller) Engineer sat in the crashed ship and was killed by a xenomorph?

Answer

Prometheus and Alien deliberately share a lot of themes, as well as the same universe, but they are not directly prequel and sequel (spoilers follow...)

1. The Space Jockey in Alien is old enough to be fossilised. Possibly by the same events that wiped out the Engineers in Prometheus (2000 years ago according to Shaw's carbon dating) but too close to Alien's dates to be the same one.




2. The planets have different names: LV-223 in Prometheus and LV-426 in Alien.




3. The planets have different atmospheres - LV-426 is "primordial" while LV-223 is "almost breathable" except for the too high CO2, which is not the case in the pyramids.




4. There are no alien structures on LV-426.




5. The ship in Prometheus is carrying black goo vases, but no eggs. The one in Alien lots of identical eggs, but no black goo.

So what is the same?

1. The Space Jockey in Alien is a giant 'human' in a suit.




2. The black goo is the source of both the alien in Alien and the various things in Prometheus. The DNA of its victim species has some effect on the result, and the final result in Prometheus is approaching the alien from Alien.




3. The eggs being carried by the crashed ship in Alien are probably the result of the black goo on something other than human, maybe something that layed eggs instead of giving birth.




4. I think that the ship in Alien is another attempt to wage biological warfare by the space jockeys/engineers. Either the eggs are before or after the black goo - both obviously went wrong so it's hard to guess which attempt came first.




5. The space jockeys/engineers share humanity's propensity for building really stupid ways to kill each other, as well as our DNA.

Ridley Scott has said that he envisions Prometheus as a trilogy, so maybe this gets tied up somehow.