a few small remarks/reminders to re-set the discussion in right track :
Eurocontrol did not set the route charges rules, the individual States that made the CRCO did that . Eurocontrol was asked to manage the scheme, i.e to act as a tax collector for the States.(it keeps 0,3% for that, the rest goes back to the member States)
One of the CRCO aims is to have equality for fair competition in Europe : everyone should follow the same rules, and pay according same rules.
The formula is based on Maximum permissible take off weight (*) , as it is based on " ability to pay" rather than be billed for the actual cost of the service .
The questions remaining in this case are , which MTOW is on the certificate of registry ( or noise certificate ) and were the FR cases mentioned by Germany just " errors" or a systematic strategy to avoid paying the full charges.
(*) the MTOW to be declared must be the highest weight authorised by the State of registration.