Generally if both ports are on the same side of the intercooler, less surface area of the cooler gets filled. The turbo obviously still has to fill up the whole intercooler but the vacuum of the motor sucks some air out before it can fill up the the other side of the i/c. Effectively what happens is you give the air less time in the intercooler because it just flows from the top to the bottom. Ideally you want to have the inlet and outlet on opposite ends so you have linear flow across the whole width of the i/c.