Don't put anything on weapon/armor displays in your ship, you will lose the items sooner or later. Doesn't even have anything to do with changing the ship's build, it'll just disappear as you come and go normally too.
Update on this, Isolation appears to be completely broken. Sucks, I was intending to go that route too. From what I've seen of other people complaining, it sounds like all the companions piss and moan about anything you do that's 'illegal'. Which means you either bring Vasco who is too fucking big, take the adoring fan trait and adventure with him, or go it alone. Not a hard choice really. I don't even miss their carry capacity with +40 from suit, +20 from pack, -50% weight of weapons (since they're already the best val/wgt ratio), and points in Weight Lifting.