Started toying around with this idea for my fanfic trilogy installment (I wanted something crazy like The Fountain + The Matrix LoL 8-} ). Anyway, I was so busy researching & trying to wrap my head around it that I didn't see the obvious connection to Prometheus: Hologram Tech!
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Compare to the Holographic Universe idea:
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From Weyland Corp's Timeline:
HOLOGRAPHIC ENVIRONMENT SIMULATOR (September 6, 2024)Weyland Industries makes first foray into the luxury goods market with its Holographic Environment Simulator. It is the first HES able to accurately recreate the aesthetic, mood and sounds of any place in the known world, as well as provide live video feed from any calibrated receiver.
Interestingly, the Engineers had also mastered this tech (seemingly interactive :O )

Nutshell: All information of 3D existence may be stored in a 2-dimensional surface area.
Compare orthographic projection (a means of representing a 3D object in 2 dimensions).

To Metatron's Cube (2D representation of all 3D Platonic solids)

To the structure of the vacuum of space (3D - star tetrahedron)

This was cool b/c I already had Metatron in my Paradise draft because of his role in creation according to the Kabbalah, and I thought it was a happy coincident that David was meeting him & the Star of David is in Metatron's cube. Anyway I didn't realize until later, that this might actually be a thing in Prometheus = the rubix cube as Metatron's cube & the symbols on the squares that Holloway presses w/his finger look a lot like the Weyland symbol on David's finger from the viral ad (he presses the screen - which is our field of vision, as if to say "your entire reality is actually a hologram!").

I found some really good videos on the hologram idea:
ETA: This is the first one I saw. It's really short (28 mins) & he goes into the idea that the brain might also function based on this principle.
This one is really good if you have the time to watch it (1:30:00) I really recommend it b/c they explain the crux of the dilemma w/Hawking's work on black holes (it had implications that contradicted the foundations of quantuum physics).
6:33 - Panel introduction
8:46 - One minute primer & beginning of discussion
Leonard Susskind is on the panel of the above video - he's pretty famous in this field.
Length: 55 mins
Talk starts @ 1:30
David is closely associated with all the holograms in the film - the PIE lessons, the violin girl signal, Weyland's "ghost" presentation, and he even figures out how to activate the Engie's hologram tech.
Javablue - this seems to go with your simulated reality theory :-bd but I propose a slightly different interpretation; instead of continuity errors being glitches in a matrix/none-of-this-is-really-happening scenario created by the engie/alien intelligence, what if history is stored as information somewhere, and if you can find where that information is stored and change it, you can change history (at least, that's what I'm gonna do for my 3rd script lol :P I figured if all the holograms we see are representations of history [violing message = human history] [pie lessons = history of language] [Weyland's "ghost"] [Star Maps = Archaeological digs] [engie holograms = recordings from the past], then maybe history is information, and if that's so, there might be a way to change history that doesn't rely on the usual cliched, tropey-time-travel stuff). Or maybe my theory is not really at odds with yours :-? I gotta think about this more, but I'd love to hear your thoughts about the possibility of a hologram reality.
PS - Ridley shooting the film in 3D @-)