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.
Haha, yeah, but if your front locomotive gets defected (windshield cracked by treebranche, truck hits front signal light, trainradio defect, etc.) and your second engine is facing forward, too, you could likely just switch their position in the train.
Either way, better hope nothing happens. (Or else I should perhaps butter the plate side of my toast, so when it accidentilly falls, it will land with the buttered side up.)
There is no perfect way to arrange multiple locomotives. In general, the "front-back" seems to have more advantages than the "front-front". As an aside, when freight locomotives are all facing front they are said to be "elephants".