Ryn operates with variable MTOW: 66,990; 69,990 and 74,990: you just need to declare which one you use prior to operate the flight.
If the rules say you need to pay according to the highest MTOW the airframe is certified for, than that's what you need to declare every time to the airport authority and pay accordingly. According to the German DFS Ryanair did not comply with this rule at least on several occasions.
As stated previously, ATOW has nothing at all to do with en-route charges.