I'm late around here with this, but I'm really surprised to find that I've never yet come across anyone mention what turned out to be one of the biggest problems I had with the 'flute' scenes in AC...
It was something which immediately distracted me and took me 'right out of the movie' at the time - it's the fact that at one point, Ridley actually had him play some of the PROMETHEUS 'Main Theme' score! :-
What the heck?, I mean this seemed like an unnecessary 'breaking of the fourth wall convention' to me, and just another bad 'creative choice' in the overall movie. But as no-one elsewhere seems to have brought this up as far as I know, I wonder if this means that everyone was fine with this particular 'callback', or even considered it to be a clever reference of sorts?
Personally, it bothered me a lot...as I usually look on movie soundtracks as being something totally separate in the background that to the overall movie footage, rather than actually being something that is 'referenced' in the movie itself - it's as if the 'cantina band' in the original STAR WARS had played John Williams' 'Main Theme', for instance, But I'm curious to see if others are as fazed by it.
Not to worry though, because I'm just going to remove the 'Engineer flute-playing' shots from PROMETHEUS for myself
(just as Agent 9 did in his great re-edit), and I'm also intending to remove this particular scene from the movie too, so that I can more easily watch these movies as an 'alternative universe' reinterpreted storyline to what occurs in ALIEN/ALIENS.