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

At the end of rel="noreferrer">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 href="http://www.imdb.com/title/tt0078748/" rel="noreferrer">Alien, the
team that explores the derelict ship discovers the body of an Engineer
pilot:

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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?

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class="normal">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.