From the Boeing website article I posted above (edited for brevity)
...Boeing began studies on converting the propeller-driven model 367 Stratotanker ... into a jet-powered tanker... product development went through several renditions of the model 367, and ... a version numbered 367-80 was selected ... The goal was to put the airplane into production as both an Air Force tanker/transport and a commercial jet transport. Since both of these ... would be jet transports, the model number system called for a number in the 700s... The marketing department decided that "Model 700" did not have a good ring to it ... [s]o they decided to skip ahead to Model 707 because that ... seemed a bit catchier.
Engineering bureaucracy spiced up by marketing!
Incidentally, the last two numbers in a Boeing model number work differently to an Airbus model.
Boeing uses a customer number: the '1R' in 747-41R means that the 747-400 was made for Virgin Atlantic.
Airbus uses an engine manufacturer id and version, so an A340-313 is an Airbus A340-300, the '1' means that it uses CFM Interntational (SNECMA/GE) engines, the last '3' means the engine model is 56-5C4