Once you drill the LIM, the rear PCV is all internal in supercharger. The intercooler blocks the front PCV. The nipple on the back of gen 5 pointing up is actually part of the (blocked) front PCV.
With a intercooler installed it is blocked from making the connection to the front PCV hole.

Connect front valve cover or oil fill extension to the TB. Cap the nipple on the back of the gen 5 supercharger.