I think the top floor is there because the crew cabin has to be high so the nose can swing up. The cables and wiring from the cabin can't be easily disconnected to allow such access. You will notice other large cargo variants of airliners load cargo only through the side of the fuselage.
Yes and no. The C5 has an upper level too. The whole setup solves a lot of problems at once. Opening nose makes for faster cargo operations which the military cares about for a bunch of reasons. There are usually people associated with military cargo so might as well seat them up there.
Any large cargo aircraft has primary loading inline with centerline, side doors just aren't efficient. It's either via front, via rear or both.
Me321/323 was I think first heavy cargo with nose clamshell doors, but after that everyone settled on nose rising up, clamshell rear. It also had the top deck.
I understand that for the 747, they initially just had a cockpit bulge atop the fuselage. However, this created too much drag, which they reduced by extending the bulge aft. They didn't need this space for flight operations, so it was naturally then used for additional passenger space.
For context, when the 747 was being developed, simultaneously Boeing was developing the SST, Britain and France were developing Concorde, and the Soviets had their own supersonic Tupolevs in development. Boeing was anticipating that supersonic aircraft would render the subsonic 747 obsolete for passengers overnight, so it was designed to be easily convertible to freight.
