You're right in that the long distance routes don't really make sense on their own, but if you view them as a bunch of shorter commuter routes which happen to be there anyway, then connecting them up tip to tip with a daily "long distance" route makes a lot of sense. To the commuters, it doesn't matter that one of the trains they might board on a given day will continue going long after they get off. But the benefit (aside from connectivity) is that the long distance sleeper car passengers are the most profitable customers the railroad has. Those people in the front of the train with their private rooms and chef made meals effectively subsidize the daily coach class commuters in the back of the train. The trick to it is getting the long distance route time table lined up so that it is coincident with its second purpose as a commuter service when it gets to whatever metro area.