The PCV line goes to what you're calling the black box, SVO. The black box on the back of the B2 is not a charcoal canister...it's just a vacuum plenum. The charcoal canister is a cylinder mounted on the firewall of the Civics.
On Civics, the line going from the valve cover to the intake is part of the PCV system. Whoever said this replaced the breather to reduce crank case emissions is right...that's what the whole PCV system is for. When the PCV is inhaling through the crank case, the fresh air that is rushed in comes into the valve cover through this line from the intake BEFORE the throttle body [hence, no vacuum on this line]. The problem with a breather is that at high load [low vacuum], the PCV isn't really sucking anything, so emissions can bellow out of this place if you have a breather. With it routed to the intake [like stock], these emissions just go right back into the engine.
Don't believe me? This effect is amplified on a turbo car. When my Civic was turbocharged, I was running a breather [can't be sucking back in any gross emissions into a turbocharged engine

]. When I was dynoing my car and began to get into high RPM's and boost, you could see the emissions billowing out of the breather...it was amazing.