- Why is the cockpit up above the main cabin?

a: Because the Boeing brains concieved of a supersonic future for the airlines, with everybody flying the SST in pax service.

The 747 was viewed as a stop-gap and therefore destined for freighter service. The cockpit was elevated to allow for nose loading.

Bonus points: how was the height of the main cabin determined?

A: High enough to accomodate conex containers. It was actually envisioned that the same shipping containers would be used for ships, trains, trucks and planes. Nobody told them that a 20' container has a 5000# empty weight......