Tilenas
Explorer
It's not so arbitrary if you look at it the right way. Cover can stop an attack cold so it increases your defenses much like a shield does. Concealment, by mainly obscuring but not actually blocking you, doesn't specifically add to your defenses. It affects them in a may be aiming right, may not be aiming right, it's hard to see, kind of way. Plus, concealment is unaffected by the skill of the spotter while cover may be decisive or virtually irrelevant depending on the skill of the attacker.
I agree with your reasoning, it probably less arbitrary than it is inconsistent.
Still, why have a fixed d% chance when it's all a matter of perception? Why make hitting equally hard for everyone, regardless of Listen/Spot modifiers? You do get a bonus on hide checks when concealed, why not roll with that?