Perhaps you can lock up your goods with either a key or password protected lock, which can be picked or hacked via terminal. If someone tries to hack or pick the lock, you get warned and have a chance to get back to your settlement to stop the thief in progress. That could be interesting.
If you can pack up your settlement and carry it around with you, I think I'll just make a few containers, dump my loot in them when my carry limit is reached and pack the settlement up again. But that sounds too easy...
Too many questions I need answers to....