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.

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.