I agree that the original Gigeresque vision still matters and is vital to the setting. I was thinking about this thread contemplating my own campaign ( one that I began using the Leading Edge Games Alien: Adventure Game- a game that actually is a disservice to the Gigeresque vision). I dislike the "humanoid in the exoskeleton" of Prometheus, it's contrary to that vision because the suit and the humanoid are distinct. In Giger's biomechanical surrealism (like we see in Necronomicon), the suit and the humanoid are not distinct entities, they are integrated as a singular being. This differs from cybernetics or prosthetics, since neither cybernetics or prosthetics are part of the being, they're added to the being externally.
The Engineer appears integrated into the derelict- they're one- the crew and ship are not completely separate entities when active, and I imagine the ship is not entirely whole without the Engineer(s). I imagine that the Engineers are product of millions of years of manipulating their own evolution, they are "created" as bio-mechanical organisms born/grown/manufactured. Their structures and their 'tools' and 'weapons' like the xenomorph are extensions of the own process of creation. There's imagery from Giger's work concerning Alien that felt like there's a mystic/ quasi-religious ( or at least reverence) towards the life cycle of the "xenomorph". I'd extend that to all aspects of their "tools" and "structures." In my thinking, the Engineer's 'pyramid' is a temple and atmospheric processor, and they change worlds with reverence and awe reflecting that 'sex' and 'death' we see in Giger's surrealism, (creating a new habitat, while killing the old one).