Armani,
Well aside from the fact that it would still include extra switching movements to move that baggage car around, Amtrak, when it can, prefers not putting sleeping cars next to coach cars. They do this in an effort to keep coach passengers from entering the sleeping cars where they don't belong. In fact, I'm actually surprised that they don't move the cafe car next to the Boston sleeper.
Arranging things as you've suggested would not only eliminate the buffer on the NY section, but it would require every coach passenger in the NY section to walk through the sleepers every time they wanted food. And any coach passenger in the Boston sleeper wanting to eat in the diner would also have to walk through the Boston sleeper.
This would not be a ideal thing, first because of course the sleeper pax get perks that aren't provided to coach pax, like free coffee, water, juice, etc. And on the Empire Builder during the peak periods when they add an extra coach between Chicago & Minneapolis, those items do disappear very fast if the attendant puts them out.
Second, the halls of the sleepers don't provide adequate room to pass others. With the amount of traffic generated by all those coach passengers trying to get to the cafe and/or diner, it would become a big problem.