The confusion rests in the fact that there are two separate areas of concern:
1. The front of the oem valve covers are connected into the air box via a tee and subsequent tubing. The partial vacuum will take fumes and oil back into tubes. This is why there are two tubes on the catch can - one from the covers and one to the airbox. You don't need have to use both, you can deadend the connection into the catch can.
2. On the oem intake there are two tubes in the front that tie into the pcv valve. This connection is at its worse under high engine braking, where the vacuum is high and the rpms are high, it takes a lot of oil and sends it directly back into the intake, this catch should absolutely be a deadend.
All this applies to a Gen 2, the Gen 1 has the pcv valve on the cover and then it is tied back into the front of the intake.