I would hope they would have some similarities. Same universe, same corporation likely owns the ship manufacturers and developed a lot of the technology used. The Nostromo itself looked like it had been in service for 20+ years. This is only supposed to be 30 years prior to Alien, so they should have similar functional design charcteristics.
The Nostromo was used as a tug for the mine/refinery, but it may have had other uses prior to that. Still, it is more of a rough, unrefined, workers ship, whereas the Prometheus looks new, more refined, and state of the art. Perfectly fits with something a mega billionaire would do for his pet research project.
I like how the med bay equipment is very similar to the Nostromo med bay. Keeps the universe consistent.