Your supercharger setup has an advantage over the turbo set up because it doesn't create as much heat as the turbo setup, therefore, you can put any cooler pretty much anywhere as you want to.
As far as your concern about the BOV location, it won't matter on the parasitic loss. The BOV only vents out the air before the air kicks back to the blower and damages it. At the same time, the blower still needs to spin as long as you rev up the engine.
I think if the BOV is near the blower, it actually will slow down the response time of the next cycle the air will be pushed toward the TB. When the TB is closed and the BOV is open, the air will travel a long distance due to the long pipe before it'll be vented out. Also, when you press on the gas at that time, the blower will start to pressurise the new air and this new air will have to push a large volume of the old air that's still trapped inside the intake and finding its way back to the BOV that's near the blower. This is where the negative side effect is.
The good location of the BOV should be near the TB, where the old air can be vented out right away after the TB is closed. And when the blower starts a new cycle, the new air will push the old air and while this old air always tries to find its way to the BOV toward the TB, both air will go in the same direction and there's only a little conflict in the direction of both air.
So I guess you can say the engine sits maybe a cm taller than stock? 
