The initial reason for putting the engines in pods out in front of the wing was - interestingly enough - structural. Turns out that the engines can be used as 'tuned mass dampers' to reduced/eliminate flutter concerns. This had the additional benefit of giving physical isolation between the engines, so that something like an uncontained failure was unlikely to damage another, adjacent engine.
Boeing then discovered - using the Boeing Transonic Wind Tunnel (BTWT) referenced earlier - that it was important to put the engine well below wing - otherwise you would get 'interference' drag where the jet exhaust combined with the airflow around the wing to create areas of trans-sonic and supersonic flow (i.e. high drag). I don't ever recall hearing any reference to the engine pod placement with respect to 'area ruling'.
Way back when we were doing initial development of the 767, they did some BTWT testing that showed serious interference drag at cruise (as in ~2% of total aircraft drag). The setup for this testing was interesting - they did a 'blown nacelle', where high pressure air was piped up through the wing and strut and exhausted out carefully crafted core and fan nozzles (I was involved in some of the blown nacelle testing). Flow vis showed there was a 'pinch point' on the inside of the strut where the combination of fuselage, nacelle, and strut resulted in something of a nozzle effect with big shocks forming. They discovered that by reshaping the strut they could open that space up enough to make the resultant interference drag unmeasurable.
Megan - your points about area ruling are good, but remember the aircraft you referenced were designed to fly much faster than (subsonic) commercial aircraft. What wasn't well understood in the 1960s is how applicable area ruling could be in the low transonic region.