En-route charges are by the declared MTOW, landing fees at BHX (when I used to calculate such things for ad-hoc's) were also based on the declared MTOW for each registration as found in JP Airline Fleets, or from the operator. Charging fees for any of the larger aircraft types at a fixed rate would cause major problems as the structural MTOW can vary by 9 tonnes on a 757, and much more the bigger the type. Would you be happy paying the same as a HGW model when you were operating the light weight? Any variation was always filled with the CAA on a flight by flight basis to ensure correct charging.