I understand that the upper deck bulge is there for aerodynamic reasons and was intended as a crew rest area. Pan Am made it into a lounge for 1st Class, so that everyone had two seats for the flight. It was not long before that idea was ditched!
I have also heard that the flight deck was put up top, to allow for the freighter version to have it's lift up nose and load wide palletts from the front.
But I sit to be corrected.
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"I tell you, we are here on Earth to fart around, and don't let anybody tell you any different." Kurt Vonnegut, Jr.