The point of the picture was to show how much you CAN'T see the factory manifold...
As for the intercooler placement, I'm going to be ducting it from underneath to the front, so the air will exit out the top. this is different than a typical top mount since they generally use a scoop to pull air down into the engine bay. I know it's more of an inter-heater right now, but it's not finished yet...Not that it matters, but the car this intercooler came off of was a 93 Sentra with the SR20DET swapped from the Pulsar and converted to 2wd with an SE-R tranny...It was doing 12.98's in the quarter mile set up exactly the same way with no duct or scoop.
As for why, look at the rest of the car, and then answer: "why not?"