What would be the point of having the player choose starting gear if the game is just going to take it away immediately and leave you with only starter armor, no weapons or other items.
It just makes the most sense to have the characters start with no weapons and equipment other than armor. If they made us naked, then they'd have to redo cutscenes so that Lae'zel and Shadowheart were also without their armor, and that would be bad.
Nah. In a rush, the mind flayer port magic that ports you into the pods strips you of all potential weapons, but it does not strip you of what you are wearing. So no pack of items, no weapons, and no shields. Then, as you explore the ship, you find some basics in the first two chambers. You know, like you are an escaped prisoner needing to find stuff to help you escape, as the story suggests?