Use of flexible MTOW has been around for years and used by many operators. Key to this issue is the interpretation of the EuroControl requirement that "the MTOW to be declared must be the highest weight authorised by the State of registration". Based on previous experience, this is typically accepted as being the MTOW stated on the individual aircraft's Noise Certificate (carried on board).
From other posts, it would appear that the IAA may have agreed to this being 66,990 kg and thus the Noise Certificate is likely to state this and not the "optional" higher MTOWs quoted of 69,990 or 74,990 however, if this is the case, then it is not clear how the aircraft could have been operated at a MTOW higher than 66,990 (which seems to be being suggested in the newspaper articles) without reference back to the IAA and issue of a revised Noise Certificate at the higher approved MTOW. If the MTOW on the Noise Certificate is either of the higher figures then it would seem this higher MTOW should have been declared and be the basis for the navigation charges to be made.
The other possibility is that the Noise Certificate does state 66,990, and this has been adhered to, and the DFS is looking to use another basis to determine the highest weight "authorised" by the IAA. Maybe they can see the higher MTOW listed in the AFM or Operations Manual and are making the interpretation that, as also IAA "authorised" documents, these can be used to support their position that the charges should be higher.
The interesting thing to know would be the figure quoted on the Noise Certificate.