I would say it really doesn't.
Having a known target would mean that you at least know what square they're in, even if you're firing with disadvantage. When you don't know what square they're in, it's an automatic miss. But again, that assumes you know something is there in the first place.
According to the PHB (page 196), a target with total cover can't be directly targeted by an attack or a spell. Which means you have a 0% chance of hitting them, doesn't it?
So, really the chances aren't the same.
There's a difference between cover and concealment. If someone is completely behind a stone wall (cover) they can't be targeted at all because the wall stops the effect. If they're hiding in the forest undergrowth or a shadowy corner (concealment) they can still be targeted (provided their location is known) but the attack is at disadvantage.
I do agree there is a distinct difference between guessing at a square (and automatically missing if you're wrong) and knowing which square but still not being able to see.