It's fitting that some of HR Giger's design work for Dune should end up in Prometheus. After all, it was his time on Jodorowsky's failed project that brought the Swiss surrealist into contact with Dan O'Bannon, who would go on to write Alien (originally titled Star Beast!). Giger's pre-existing paintings were crucial in the development of the look of Alien - Necronom IV, painted in 1976 gives the initial design of the Xenomorph while Necronom V (same year) gives the first form of the Space Jockey (now known as The Engineers). While Giger did come on board and consult and design further, those two paintings form the backbone of Alien.
In the excellent, gorgeous book Prometheus: The Art of The Film (which you should buy at the link at the bottom of the article) art designer Arthur Max says that they went back to some of the original Giger work for the design of the mysterious pyramid. They began with this image:
which was Giger's original vision for the structure where the Xenomorph eggs are discovered. That eventually changed into the familiar crescent ship, which also appears in Prometheus.
In the book Max says:
We went more toward the mechanical forms that were included in his architectural style. Giger's design is very clearly organic. It looked like a pig's bladder, inflated. We took the organic nature out of it, and made it more of a rock formation. The challenge was to deconstruct Giger, taking his forms and purifying them. There are motifs that are revisited, but, hopefully, subtly so it doesn't distract you.
The book includes this image on the facing page, one that is a not so subtle revisited motif.
But not from Alien! It's an image that really calls back to Giger's design for the Harkonnen Castle from Jodorowsky's Dune:
Cellulord has some nice comparison images of Giger's Dune designs with finished work from Prometheus:
And so it all comes full circle. It seems fitting. And makes more narrative sense than Prometheus itself.