You just found the only way the CP can take the oil "directly" to the refinery, it involves a barge.
Very good point!
I can't see how this could be anything more than a temporary solution to meet Bayway's needs until their rail infrastructure is built/expanded. The rail routing will inevitably be longer (and more expensive) than a direct route as it will probably take the scenic route via Montreal and head due south from there to Albany. Then there would be additional costs involved with the transload and barge expenses.
If they really do build a rail yard with unloading capacity, I'd say they will slowly change all of their routings to direct shipments in the future.