If you guys ever played Warframe, there's these ships called Corpus Crewships, whihc can be entered an explored by the player during certain missions. They're basically large, rectangular ships with a lot of verticality to em. Since the Harvester has a similar shape, i was thinking that, if you guys ever think of opening up the the main hub a bit more, you could take inspiration from the Crewships.
When entering one, there are 3 floors/sections you can travel through by stairs or elevator (or just by Bullet Jumping, in Warframe's case). The center part usually differs, and will either have debris, cargo crates, or stored robotics, all held on the inside scaffolding. On the very bottom is the Crewship's reactor.
Now, imagine of the Harvester's interior was designed in a similar way, with numerous floors that contain different functions of the ship. The bottom floor could be like, Meat/Fuel Processing, where harvested meat is processed in fuel for the Harvester or converted into Smart Meat to create more Meat Scientists, while tother could be for weapon R&D or body part storage. You could also add, like, meat hooks that act as quick transversal points that will quickly take you from the bottom to the top floor of the Harvester.