Made an interesting discovery while searching for reference pictures on the Net...H. R. Giger's concept for the Harkonnen Dome wasn't the only thing related to an attempt to film Dune that looks like it was used in Prometheus. The Engineer egg chair from the Orrery controls looks a lot like designs Giger made and had built for a 1979 filming that ultimately never came about. If events had gone differently - Ridley Scott and H.R. Giger would have designed and produced Dune as well as (or maybe instead of) Alien.
I also would consider similarities between the 1984 Fremen stillsuits and the Engineer pressure suit, but those could be as much anatomy textbook as anything else...