I've been doing a similar thing...if I leave a rifle in my Pisces and self-destruct, I then get a square box half the size of the one you got (yours was rectangular).
That makes it easier to move around via tractor beam inside the bunker and collect & store the gear off the dead bodies.
The box persists when I store the ship, but if you have to claim the ship, then you will lose it.
Also, due to weird server issues this week and 30k's, I highly recommend you empty the box into your local planet or station storage **as soon as you land**, just to make sure you don't lose all your hard stolen swag!