Prometheus, being an interstellar ship, also acted as an orbital shuttle for the crew. in original Alien, at least Scott Riley had the sense to park the cargo ship in the orbit, and used the shuttle to land on the surface.
it's also ridiculous that during the storm, they raced back to the ship to escape the storm instead of hideout in the U structure. i was surprised to see that the ship escaped the crazy storm unscathed.
In Alien they used the Nostromo cargo-tug to go down, detached from the factory/mining/ore-hauling part. The small shuttle/lifeboat that Ripley escaped in at the end was a separate thing.
Also, the "life pod" was designed to support someone(s) for a considerable length of time. A shuttle wouldn't be. In a way, it was something of an unlikely plot glitch that the shuttle in Alien had a cryosleep chamber, conveniently just for one person.
if we trusted the fansite, here's the specifications of USCSS Prometheus:
Manufacturer
Weyland Corp Product line
Weyland FTL ships Model
Heavy exploration/prospecting vessel Class
Heliades-class Cost $1 trillion
Technical specifications Length
130 metres (427 ft.)[1] Width
48.75 metres (160 ft.)[1] Height
36.5 metres (120 ft.)[1]
this is typical that the sum of all parts is bigger than the whole, we see from the film that the ship have hibernation chamber, mass hall, cargo bay, bridge, sleeping quarters, cafeteria, charlie theoron's private chamber and medical bay, weyland's secret chamber, etc. it's amazing they fit all those into a 130m long ship, space shuttle is bigger than that but more crowded inside
"this is typical that the sum of all parts is bigger than the whole,"
To me what you are not taking into account is that the Prometheus ship had multiple levels. While this isn't a 120 foot tall building, such a building could have 11 stories. http://www.convertunits.com/from/feet/to/story
Since the Prometheus is a space ship, there is much less room than that (due to the height of the landing gear and the thickness of the hull). But there is still enough space for at least three levels. The habitat area of an Airbus A380 airliner for instance is much smaller than the Prometheus ship and the Airbus has two passenger levels and a cargo level. https://en.m.wikipedia.org/wiki/Airbus_A380
For instance with the illustration at the bottom of the page of the Prometheus ship, it shows that the medical bay and cargo bays are at a the lowest levels. The Lifeboat (with the Medpod) is at the end of the ship.