There are dramatic differences in technological aesthetics and anatomy between the engineers across Alien, Prometheus and Covenant. The differences are extreme enough that they do not look like members of the same species.
Among other things (see the attached image for a side-by-side comparison of anatomy), the engineer in Alien is at least twice as large as those in the prequels, does not have legs or any room for legs that are not broken, and is fused with or growing out of the pilot's seat.
The technology in Alien is biomechanical in nature, resembling a weird cross between industrial machinery and bones and mummified bodies. The technology in Prometheus and Covenant is clearly artificially constructed, but it seems to be aping the aesthetic of Alien. The design of the juggernaut/derelict cockpit is different, as the one in Alien does not seem intended for walking around, since the floor is full of holes and there are no stairs; whereas the one in Prometheus has a flat surface and a convenient staircase.
In Covenant, the engineers bear little physical resemblance to the one from Prometheus. They appear to be a different species, but they use the same technology.
I am aware that in the prequels the engineers are revealed to be humans wearing suits. This is supposed to be a retroactive change applied to the pilot from Alien. That does not explain the obvious disparities in anatomy and technology. I know that these inconsistencies are a result of sloppy production, but I will assume that these differences exist within the fictional universe rather than continuity errors.
This is what the original pilot seat of the derelict ship in Alien looked like:
Based on the shape of the suit and the general Giger aesthetic, the pilot in Alien should look something like this:
The engineers in Prometheus look like this:
The engineers in Covenant look like this: