I have a similar gripe where you make customizations to the ship and everything you had placed around the ship and in separate containers is all moved to the overall cargo hold of the ship. I get why they did that because it would be ripe for exploits and other weirdness.

The other issue is that sometimes I like this because it gets rid of the clutter around the ship like the random little useless items that you’ll never actually use. I don’t care to have that stuff everywhere. But you go offload it for the credits and then a few days later, everything is back the way it is.

There is an exploit to be had here in that you can do this a bunch of get infinite credits by selling all these items every so often they reappear.