If you look closely at the second shot, you will see that there is a human bag near the stairs that lead the the pilot chair. No bag around when David is kneeling on the console.
The plateform is also missing those small consoles like things between sarcophagis so this not at all the same scene...
The angles are almost identical.
David kneeling shot is higher hence making him look a bit smaller.
The Engineer watching shot is a lower angle should make him look a bit bigger.
Both shots are as wide so i think it's a very good comparaison photo.
From the running holograms you can see that David is clearly smaller than a real Engineer.
Here i can clearly see that David is not at all dwarfed by the supposed Engineer