The way I remember from reading about the two designs is that the 707's fuselage shape was widened in response to the DC-8 going for six-abreast seating. At that point Boeing realised that they needed the same on the 707 and widened the upper part of the double bubble, but leaving them with two different fuselages for the C-135 and 707 families.
This image doesn't show the full fuselage shape for these types, but it is a nice comparison.
