As a fan of similar sandbox games, it always burns me up that raiding people's base while they are offline is the primary means of aggression. Rust, Space Engineers PvP servers, minecraft etc each provide some potection against players looking to raid your base while you are logged off, but it usually is not enough. Some space engineers servers had a rule of not attacking/greifing people while they aren't logged on to defend it, but it often went uninforced. With Rust, you needed either several small huts with your gear equally split up and hidden to mitigate losses, or have a huge team maintaining giant walls 24/7.
From an immersion standpoint sure, it makes sense that it would be easier to raid a zone if no one is guarding it, however scifi characters don't physically dissapear from their empites to work a 9-5.
In a traditional MMO, your character doesn't exist while you aren't loged on, however with controlled zone, there should be some type of protection. I'm guessing this is where the territory system sets in?