While I see where you're coming from, it still has its issues. Let's take Alien Isolation for example. You spend most of the game afraid of the Xeno, because at any moment, it could show up, and you know you can't outrun it, or hide from it if it spots you. However, by the time you get a flamethrower and can actually defend yourself, like the Xeno is hardly a threat, it becomes less scary and more annoying to die by it. My point is, if there comes a point where defense is an option, suspense and the feeling of helplessness against a superior enemy goes away.
From the start, we see our base as a safe haven, but as we progress the game, we realize how little locking our doors even does, as if an entity wants to get in, they WILL get in. That's just how things work. We aren't meant to be defending ourselves, but we are meant to be experiencing the horror set out in front of us. We are helpless, alone, and can't call for help. That IS the horror of the game. Not just because it has spooky aliens in it.