Well I mean it doesn't really matter which way the rear locomotives are facing. But if one is facing forward and the other is facing backwards, in case something happens and the train now needs to go back the opposite way, there is no need to wye the engines, as they can easily be moved to the back.
Example: Due to a freight derailment in Idaho, the eastbound Empire Builder will end at Spokane and the westbound Empire Builder will end at Whitefish. The passengers will be bussed from Spokane to Whitefish or vise versa and board the train there. So basically they will turn the train at Whitefish and Spokane, respectively. If the locomotives are facing opposite ways, they can easily bring them to the back (now front) to bring the train the other direction.
Hope that made sense...