those are all known vanilla bugs, some information about your owned ships does not get saved and loaded correctly, the game treats your owned ships as captured after reloading and some of the npcs ships as your own. Hopefully will be fixed in the next patch.

Nevermind the part about not updating the equipped ship. Apparently, it created a different packed ship when i docked with the cargo saved in that packed ship. Might be because earlier i had to hack my own ship as if i was capturing it for the first time after reloading a save when i was on board an event-spawned ship (the pirate ship that starts the mission to go to the red sector). The poke... "packey ball" item was refusing to activate, saying that the ship was already spawned from a packed ship in my inventory. Honestly, idk what mod, if any, caused that weird interaction to happen. Might have been this mod, alternative hacking, community bugfix, or just random vanilla spaghetti code. Oh, and sorry for the three headache inducing walls of text in your comment section.

Also, if you use the hangar with a different ship to the one currently equipped, it also gets deleted, and does not generate a packed ship. Though, that might be a vanilla bug, as my inventory was full when i docked.

Finally, the nuisance of needing to run to your ship every time your inventory fills up when looting is eliminated! There might be a bit of an issue, however. This mod seems to break the docking hangar, making it so your currently equipped ship's inventory does not update when you dock, which means everything that was in the ship's cargo gets deleted from existence upon docking.