"How do the powers that be decide on what the pay rate for a certain airplane should be?"
The answer goes back to the "good old days" when heavy jets were first introduced into the airline's fleets.
The advent of the jet brought with it an increase in hourly productivity for pilots. For management they could haul more people and freight further and faster than ever before which meant for the pilot, doing more "work" in the same amount of time. Thus the gross weight and airspeed formula was developed. Also there was a premium pay hold over from night and over-water flying which was considered more hazardous.
Essentially the reason heavies and wide bodies pay more was because they weigh more. Additionally, a single wide body jet has the potential to gain more revenues than two of the earlier narrow body airplanes.
The answer then is simply this, productivity and revenue generation potential. Of course all of this has been forgotten.
Merry Christmas!