Some Logic/Setting Uncertainties

Greetings, Here are some points of uncertainty for me that I would love to have clarified by a qualified expert; 1) Is the Ampule room part of the SJ Ship or just a section of the temple that acts as weapons storage bunker? Are the similar looking temples behind the one Prometheus explores filled with unique weaponized species and Ships as well? 2) Was the egg-chamber found by Kane in Alien (which seems based on the ampule room) part of the derelict ship on LV-426 or was it a storage depot below the craft. It doesn't seem to visually fit the shape or size of the Ship as viewed from the exterior. 3) Does each ampule in the Sj Temple contain unique evolutionary accelerant, or is it all the same weaponized goo? Some of the ampules seem to be different shape/size. 4) Why can the Prometheus away team not wear a helmet in the temple, but must wear them outside of the temple? Does this imply that Sj's breathe the same air as humans? Does this point to SJ's and Humans being the endpoint of the evolutionary cycle? 5) If the worms were indigenous to LV 223 & the cobralien was the end product of accidental leaked goo, (thus making the harmless worms into weaponized cobraliens) is it safe to assume that the cobraliens on LV223 killed other Sj pilots and caused the Last Engineer to flee to Cryo?