Ridley was keen to leave the viewers on the edge about what they had seen due to the constraints of the film budget and time, and maybe he would have been able to go into details about the alien races from an anthropologists point of view in the sequel, which he never directed and so never had any answers to spill forth on the Alien matter to spill forth in a movie form. He was content to allow it to be debatable whether the pilot was an integrated part of the vessel or a separate entity that had ossified into its seat, and that the pilot's chest hole had been created by a chest buster bursting from an infected pilot, or a half grown alien creature had punched a hole into it's chest and pulled something out since it was too young to pull the Jockey's body away to be cocooned. He didn't try to define what the thing was that the jockey sat behind. These things remained as variables, although Giger who had designed it assumed that it was a telescope, despite this unending mystery, later.
Scott was keen to emphasize basically "clearly from here this is where the transmission would emanate from probably in an automatic transmission, so this creature obviously had experienced a, maybe one of the eggs had been disturbed, and a creature had got out, had attacked the rest of the crew, don't ask me where they got to." (Alien, 30th Anniversary DVD commentary)