One is an intake and one is an exhaust. The idea is not simply to relieve pressure that builds up in the crankcase, but to ventilate it "positively" (which is what the "P" in "PVC" stand for). In the set-up you describe, the oil filler cap is the exhaust, and the oil trap is the intake.

There is no difference in pressure, but that routing is supposedly slightly more efficient that the reverse hook-up, because convection helps clear the fumes.