Part of me wishes that inventory was tracked separately between ships, and content was kept persistent when you swap them out. I get that the shared inventory is convenient, but it also just feels very weird when what you're really doing is building a fleet of ships that should still exist persistently.
It's almost like they want you to really just build one personal ship and stick with it, but on the other hand they keep throwing you into scenarios where you are made to pilot different ships that automatically change what your home ship is.
Since the cargo modules themselves are basically just shipping containers slotted into standard-size holders, why not just do it the old fashioned way, have inventory tracked per container, and let players choose to move the ship inventory from ship to ship while keeping the interior contents persistent for each ship?